1const MAG_PIPELINES = [ 2 { 3 "id": "pipeline1", 4 "name": "ancient DNA", 5 "attributes": { 6 "qc": [ 7 "FastQC", 8 "fastp", 9 "BBTools" 10 ], 11 "assembly": [ 12 "Bowtie2", 13 "MEGAHIT" 14 ], 15 "binning": [ 16 "CONCOCT", 17 "MaxBin", 18 "MetaBAT" 19 ], 20 "qualityAssessment": [ 21 "CheckM" 22 ], 23 "refinement": [ 24 "DASTool" 25 ], 26 "taxonomy": [ 27 "GTDB-Tk" 28 ], 29 "functionalAnnotation": [], 30 "other": [ 31 "mapDamage2" 32 ] 33 }, 34 "description": "ancient DNA pipeline.", 35 "url": "", 36 "details": "", 37 "category": "Metagenomic MAG Reconstruction Pipelines" 38 }, 39 { 40 "id": "pipeline2", 41 "name": "Anvi'o", 42 "attributes": { 43 "qc": [ 44 "Illumina-utils" 45 ], 46 "assembly": [ 47 "metaSPAdes", 48 "MEGAHIT", 49 "IBDA-UD" 50 ], 51 "binning": [ 52 "MetaBAT2", 53 "CONCOCT", 54 "MaxBin2", 55 "BinSanity" 56 ], 57 "qualityAssessment": [], 58 "refinement": [ 59 "DASTool" 60 ], 61 "taxonomy": [ 62 "KrakenUniq", 63 "Centrifuge" 64 ], 65 "functionalAnnotation": ["DIAMOND (NCBI COG)", "Pyrodigal", "HMMER"], 66 "other": [ 67 "" 68 ] 69 }, 70 "description": "Anvi'o pipeline.", 71 "url": "", 72 "details": "", 73 "category": "Metagenomic MAG Reconstruction Pipelines" 74 }, 75 { 76 "id": "pipeline3", 77 "name": "Aviary", 78 "attributes": { 79 "qc": [ 80 "FastQC", 81 "Filtlong", 82 "NanoPack2", 83 "SingleM" 84 ], 85 "assembly": [ 86 "metaSPAdes", 87 "MEGAHIT", 88 "metaFlye", 89 "Unicycler" 90 ], 91 "binning": [ 92 "MetaBAT2", 93 "MetaBAT", 94 "MaxBin2", 95 "VAMB", 96 "CONCOCT", 97 "Rosella" 98 ], 99 "qualityAssessment": [ 100 "CheckM", 101 "metaQUAST", 102 "CoverM" 103 ], 104 "refinement": [ 105 "DASTool" 106 ], 107 "taxonomy": [ 108 "GTDB-Tk" 109 ], 110 "functionalAnnotation": [ 111 "Prodigal", 112 "DIAMOND (eggNOG)" 113 ], 114 "other": [ 115 "Lorikeet" 116 ] 117 }, 118 "description": "Aviary pipeline.", 119 "url": "", 120 "details": "", 121 "category": "Metagenomic MAG Reconstruction Pipelines" 122 }, 123 { 124 "id": "pipeline4", 125 "name": "BV-BRC", 126 "attributes": { 127 "qc": [ 128 "TrimGalore", 129 "BBTools", 130 "BLAST" 131 ], 132 "assembly": [ 133 "metaSPAdes", 134 "MEGAHIT" 135 ], 136 "binning": [ 137 "PATRIC metagenome binning service" 138 ], 139 "qualityAssessment": [ 140 "EvalG and EvalCon" 141 ], 142 "refinement": [], 143 "taxonomy": [ 144 "RASTtk" 145 ], 146 "functionalAnnotation": [], 147 "other": [ 148 "VIGOR4", 149 "Mat_Peptide" 150 ] 151 }, 152 "description": "BV-BRC pipeline.", 153 "url": "", 154 "details": "", 155 "category": "Metagenomic MAG Reconstruction Pipelines" 156 }, 157 { 158 "id": "pipeline5", 159 "name": "DATMA", 160 "attributes": { 161 "qc": [ 162 "Trimmomatic", 163 "FastQC", 164 "FLASH2", 165 "BWA" 166 ], 167 "assembly": [ 168 "metaSPAdes", 169 "Velvet", 170 "MEGAHIT" 171 ], 172 "binning": [ 173 "CLAME" 174 ], 175 "qualityAssessment": [ 176 "CheckM" 177 ], 178 "refinement": [], 179 "taxonomy": [ 180 "BLAST", 181 "Kaiju" 182 ], 183 "functionalAnnotation": [ 184 "Prodigal", 185 "GeneMark" 186 ], 187 "other": [ 188 "Krona" 189 ] 190 }, 191 "description": "DATMA pipeline.", 192 "url": "", 193 "details": "", 194 "category": "Metagenomic MAG Reconstruction Pipelines" 195 }, 196 { 197 "id": "pipeline6", 198 "name": "EasyMetagenome", 199 "attributes": { 200 "qc": [ 201 "KneadData", 202 "HostPurge", 203 "FastQC" 204 ], 205 "assembly": [ 206 "metaSPAdes", 207 "MEGAHIT" 208 ], 209 "binning": [ 210 "MetaWRAP-native module" 211 ], 212 "qualityAssessment": [ 213 "CoverM", 214 "CheckM2" 215 ], 216 "refinement": [ 217 "MetaWRAP-native module" 218 ], 219 "taxonomy": [ 220 "GTDB-Tk2" 221 ], 222 "functionalAnnotation": [ 223 "MetaProdigal", 224 "eggNOG-mapper" 225 ], 226 "other": [ 227 "dRep", 228 "Kraken2", 229 "Bracken", 230 "HUMAnN3" 231 ] 232 }, 233 "description": "EasyMetagenome pipeline.", 234 "url": "", 235 "details": "", 236 "category": "Metagenomic MAG Reconstruction Pipelines" 237 }, 238 { 239 "id": "pipeline7", 240 "name": "EasyNanoMeta", 241 "attributes": { 242 "qc": [ 243 "fastp", 244 "BEDTools", 245 "Porechop", 246 "Minimap2", 247 "SAMtools" 248 ], 249 "assembly": [ 250 "metaFlye",
251 "OPERA-MS", 252 "metaSPAdes", 253 "MetaPlatanus", 254 "NextPolish" 255 ], 256 "binning": [ 257 "SemiBin2", 258 "MetaBAT2", 259 "MaxBin2", 260 "CONCOCT", 261 "VAMB" 262 ], 263 "qualityAssessment": [ 264 "CheckM2" 265 ], 266 "refinement": [], 267 "taxonomy": [ 268 "GTDB-Tk2", 269 "PhyloPhlAn" 270 ], 271 "functionalAnnotation": [ 272 "Prokka" 273 ], 274 "other": [ 275 "Kraken2", 276 "Centrifuge" 277 ] 278 }, 279 "description": "EasyNanoMeta pipeline.", 280 "url": "", 281 "details": "", 282 "category": "Metagenomic MAG Reconstruction Pipelines" 283 }, 284 { 285 "id": "pipeline8", 286 "name": "Eukfinder", 287 "attributes": { 288 "qc": [ 289 "Bowtie2", 290 "Trimmomatic" 291 ], 292 "assembly": [ 293 "metaSPAdes" 294 ], 295 "binning": [ 296 "MyCC", 297 "Metaxa2" 298 ], 299 "qualityAssessment": [], 300 "refinement": [], 301 "taxonomy": [ 302 "Centrifuge", 303 "PLAST" 304 ], 305 "functionalAnnotation": [], 306 "other": [] 307 }, 308 "description": "Eukfinder pipeline.", 309 "url": "", 310 "details": "", 311 "category": "Metagenomic MAG Reconstruction Pipelines" 312 }, 313 { 314 "id": "pipeline9", 315 "name": "Galaxy", 316 "attributes": { 317 "qc": [ 318 "FastQC", 319 "Seqtk", 320 "Trimmomatic" 321 ], 322 "assembly": [ 323 "metaSPAdes" 324 ], 325 "binning": [ 326 "MaxBin2" 327 ], 328 "qualityAssessment": [], 329 "refinement": [], 330 "taxonomy": [ 331 "GTDB-Tk2", 332 "CAT" 333 ], 334 "functionalAnnotation": [ 335 "Prokka" 336 ], 337 "other": ["Kraken"] 338 }, 339 "description": "Galaxy pipeline.", 340 "url": "", 341 "details": "", 342 "category": "Metagenomic MAG Reconstruction Pipelines" 343 }, 344 { 345 "id": "pipeline10", 346 "name": "GEN-ERA", 347 "attributes": { 348 "qc": [ 349 "fastp", 350 "FastQC" 351 ], 352 "assembly": [ 353 "SPAdes", 354 "metaSPAdes", 355 "Canu", 356 "metaFlye", 357 "Pilon", 358 "RagTag" 359 ], 360 "binning": [ 361 "MetaBAT2", 362 "CONCOCT" 363 ], 364 "qualityAssessment": [ 365 "CheckM", 366 "GUNC", 367 "CheckM2", 368 "EukCC", 369 "BUSCO", 370 "Physeter", 371 "Kraken", 372 "QUAST" 373 ], 374 "refinement": [], 375 "taxonomy": [ 376 "AMAW", 377 "BRAKER2", 378 "GTDB-Tk" 379 ], 380 "functionalAnnotation": [ 381 "Prodigal", 382 "Mantis", 383 "Anvi'o scripts (KEGG)" 384 ], 385 "other": [ 386 "OrthoFinder" 387 ] 388 }, 389 "description": "GEN-ERA pipeline.", 390 "url": "", 391 "details": "", 392 "category": "Metagenomic MAG Reconstruction Pipelines" 393 }, 394 { 395 "id": "pipeline11", 396 "name": "HiFi-MAG", 397 "attributes": { 398 "qc": [], 399 "assembly": [], 400 "binning": [ 401 "MetaBAT2", 402 "SemiBin2" 403 ], 404 "qualityAssessment": [ 405 "CheckM2" 406 ], 407 "refinement": [ 408 "DASTool" 409 ], 410 "taxonomy": [ 411 "GTDB-Tk2" 412 ], 413 "functionalAnnotation": [], 414 "other": [] 415 }, 416 "description": "HiFi-MAG pipeline.", 417 "url": "", 418 "details": "", 419 "category": "Metagenomic MAG Reconstruction Pipelines" 420 }, 421 { 422 "id": "pipeline12", 423 "name": "IDseq", 424 "attributes": { 425 "qc": [ 426 "Trimmomatic", 427 "STAR", 428 "Bowtie2", 429 "CD-HIT" 430 ], 431 "assembly": [ 432 "SPAdes", 433 "Bowtie2" 434 ], 435 "binning": [], 436 "qualityAssessment": [], 437 "refinement": [], 438 "taxonomy": [ 439 "GSNAPL", 440 "RAPsearch2" 441 ], 442 "functionalAnnotation": [], 443 "other": [] 444 }, 445 "description": "IDseq pipeline.", 446 "url": "", 447 "details": "", 448 "category": "Metagenomic MAG Reconstruction Pipelines" 449 }, 450 { 451 "id": "pipeline13", 452 "name": "KBase", 453 "attributes": { 454 "qc": [ 455 "FastQC", 456 "Trimmomatic", 457 "Cutadapt" 458 ], 459 "assembly": [ 460 "metaSPAdes", 461 "MEGAHIT", 462 "IBDA-UD" 463 ], 464 "binning": [ 465 "MetaBAT2", 466 "CONCOCT", 467 "MaxBin2" 468 ], 469 "qualityAssessment": [ 470 "CheckM" 471 ], 472 "refinement": [ 473 "DASTool" 474 ], 475 "taxonomy": [ 476 "RASTtk", 477 "GTDB-Tk" 478 ], 479 "functionalAnnotation": [ 480 "DRAM" 481 ], 482 "other": [ 483 "OMEGGA", 484 "ModelSEED2", 485 "Kaiju", 486 "FastANI", 487 "FastTree2", 488 "dRep", 489 "Muscle5" 490 ] 491 }, 492 "description": "KBase pipeline.", 493 "url": "", 494 "details": "", 495 "category": "Metagenomic MAG Reconstruction Pipelines" 496 }, 497 { 498 "id": "pipeline14", 499 "name": "MAGNETO", 500 "attributes": { 501 "qc": [ 502 "fastp", 503 "Bowtie2", 504 "FastQscreen" 505 ], 506 "assembly": [ 507 "MEGAHIT", 508 "Simka" 509 ], 510 "binning": [ 511 "MetaBAT2" 512 ], 513 "qualityAssessment": [ 514 "CheckM" 515 ], 516 "refinement": [ 517 ], 518 "taxonomy": [ 519 "GTDB-Tk" 520 ], 521 "functionalAnnotation": [ 522 "Prodigal", 523 "Linclust", 524 "CD-HIT", 525 "eggNOG-mapper" 526 ], 527 "other": [ 528 "mOTUs", 529 "dRep" 530 ] 531 }, 532 "description": "MAGNETO pipeline.", 533 "url": "", 534 "details": "", 535 "category": "Metagenomic MAG Reconstruction Pipelines" 536 }, 537 { 538 "id": "pipeline15", 539 "name": "metaGEM", 540 "attributes": { 541 "qc": [ 542 "fastp" 543 ], 544 "assembly": [ 545 "MEGAHIT", 546 "BWA" 547 ], 548 "binning": [ 549 "MetaBAT2", 550 "CONCOCT", 551 "MaxBin2" 552 ], 553 "qualityAssessment": [ 554 "MetaWRAP-native module" 555 ], 556 "refinement": [ 557 558 ], 559 "taxonomy": [ 560 "GTDB-Tk" 561 ], 562 "functionalAnnotation": [ 563 "Prokka" 564 ], 565 "other": [ 566 "Roary", 567 "CarveMe", 568 "SMETANA", 569 "MEMOTE", 570 "GRiD" 571 ] 572 }, 573 "description": "metaGEM pipeline.", 574 "url": "", 575 "details": "", 576 "category": "Metagenomic MAG Reconstruction Pipelines" 577 }, 578 { 579 "id": "pipeline16", 580 "name": "MetaGenePipe", 581 "attributes": { 582 "qc": [ 583 "Trimmomatic", 584 "TrimGalore", 585 "FastQC" 586 ], 587 "assembly": [ 588 "MEGAHIT" 589 ], 590 "binning": [], 591 "qualityAssessment": [], 592 "refinement": [], 593 "taxonomy": [ 594 "DIAMOND (SwissProt)" 595 ], 596 "functionalAnnotation": [ 597 "Prodigal", 598 "HMMER (KOfamKOALA)" 599 ], 600 "other": ["BLAST"] 601 }, 602 "description": "MetaGenePipe pipeline.", 603 "url": "", 604 "details": "", 605 "category": "Metagenomic MAG Reconstruction Pipelines" 606 }, 607 { 608 "id": "pipeline17", 609 "name": "Metagenome-Atlas", 610 "attributes": { 611 "qc": [ 612 "BBTools" 613 ], 614 "assembly": [ 615 "MEGAHIT", 616 "metaSPAdes" 617 ], 618 "binning": [ 619 "MetaBAT2", 620 "MaxBin2", 621 "VAMB" 622 ], 623 "qualityAssessment": [ 624 "BUSCO", 625 "CheckM", 626 "CheckM2" 627 ], 628 "refinement": [ 629 "DASTool" 630 ], 631 "taxonomy": [ 632 "GTDB-Tk" 633 ], 634 "functionalAnnotation": [ 635 "Prodigal", 636 "eggNOG-mapper", 637 "DRAM" 638 ], 639 "other": ["dRep"] 640 }, 641 "description": "Metagenome-Atlas pipeline.", 642 "url": "", 643 "details": "", 644 "category": "Metagenomic MAG Reconstruction Pipelines" 645 }, 646 { 647 "id": "pipeline18", 648 "name": "Metagenomics-Toolkit", 649 "attributes": { 650 "qc": [ 651 "fastp", 652 "Porechop", 653 "Filtlong", 654 "NanoPack2", 655 "KMC", 656 "Nonpareil" 657 ], 658 "assembly": [ 659 "metaFlye", 660 "metaSPAdes", 661 "MEGAHIT" 662 ], 663 "binning": [ 664 "MetaBAT2", 665 "MetaCoAG", 666 "MetaBinner" 667 668 ], 669 "qualityAssessment": [ 670 "CheckM" 671 ], 672 "refinement": [ 673 "MAGScoT" 674 ], 675 "taxonomy": [ 676 "MMSeqs2 taxonomy", 677 "GTDB-Tk2" 678 ], 679 "functionalAnnotation": [ 680 "Prodigal", 681 "Prokka", 682 "CARD-RGI" 683 ], 684 "other": [ 685 "CarveMe", 686 "SMETANA", 687 "MEMOTE", 688 "gapseq", 689 "Pyani", 690 "SANS", 691 ] 692 }, 693 "description": "Metagenomics-Toolkit pipeline.", 694 "url": "", 695 "details": "", 696 "category": "Metagenomic MAG Reconstruction Pipelines" 697 }, 698 { 699 "id": "pipeline19", 700 "name": "Metaphor", 701 "attributes": { 702 "qc": [ 703 "FastQC", 704 "fastp", 705 "MultiQC" 706 ], 707 "assembly": [ 708 "MEGAHIT" 709 ], 710 "binning": [ 711 "VAMB", 712 "MetaBAT2", 713 "CONCOCT" 714 ], 715 "qualityAssessment": [ 716 "metaQUAST" 717 ], 718 "refinement": [ 719 "DASTool" 720 ], 721 "taxonomy": [ 722 "DIAMOND (NCBI COG)" 723 ], 724 "functionalAnnotation": [ 725 "Prodigal", 726 "Prokka" 727 ], 728 "other": [] 729 }, 730 "description": "Metaphor pipeline.", 731 "url": "", 732 "details": "", 733 "category": "Metagenomic MAG Reconstruction Pipelines" 734 }, 735 { 736 "id": "pipeline20", 737 "name": "metagWGS", 738 "attributes": { 739 "qc": [ 740 "FastQC", 741 "Cutadapt", 742 "Sickle", 743 "SAMtools", 744 "BWA" 745 ], 746 "assembly": [ 747 "metaSPAdes", 748 "MEGAHIT", 749 "hifiasm", 750 "metaFlye" 751 ], 752 "binning": [ 753 "MetaBAT2", 754 "CONCOCT", 755 "MaxBin2" 756 ], 757 "qualityAssessment": [ 758 "metaQUAST" 759 ], 760 "refinement": [ 761 "Binette", 762 ], 763 "taxonomy": [ 764 "GTDB-Tk2" 765 766 ], 767 "functionalAnnotation": [ 768 "Prodigal", 769 "eggNOG-mapper" 770 ], 771 "other": ["dRep", "Kaiju"] 772 }, 773 "description": "metagWGS pipeline.", 774 "url": "", 775 "details": "", 776 "category": "Metagenomic MAG Reconstruction Pipelines" 777 }, 778 { 779 "id": "pipeline21", 780 "name": "MetaWRAP", 781 "attributes": { 782 "qc": [ 783 "FastQC", 784 "TrimGalore" 785 ], 786 "assembly": [ 787 "metaSPAdes", 788 "MEGAHIT" 789 ], 790 "binning": [ 791 "MetaBAT2", 792 "CONCOCT", 793 "MaxBin2" 794 ], 795 "qualityAssessment": [ 796 "CheckM" 797 ], 798 "refinement": [ 799 "MetaWRAP-native module" 800 ], 801 "taxonomy": [ 802 "Kraken", 803 "BLAST" 804 ], 805 "functionalAnnotation": [ 806 "Prokka" 807 ], 808 "other": [ 809 "Blobology", 810 "Kraken" 811 ] 812 }, 813 "description": "MetaWRAP pipeline.", 814 "url": "", 815 "details": "", 816 "category": "Metagenomic MAG Reconstruction Pipelines" 817 }, 818 { 819 "id": "pipeline22", 820 "name": "MGnify", 821 "attributes": { 822 "qc": [ 823 "Trimmomatic", 824 "Biopython" 825 ], 826 "assembly": [ 827 "metaSPAdes" 828 ], 829 "binning": [], 830 "qualityAssessment": [], 831 "refinement": [ 832 "" 833 ], 834 "taxonomy": [ 835 "DIAMOND (UniRef90)" 836 ], 837 "functionalAnnotation": [ 838 "Prodigal", 839 "FragGeneScan", 840 "InterProScan", 841 "eggNOG-mapper", 842 "HMMER" 843 ], 844 "other": [ 845 "antiSMASH" 846 ] 847 }, 848 "description": "MGnify pipeline.", 849 "url": "", 850 "details": "", 851 "category": "Metagenomic MAG Reconstruction Pipelines" 852 }, 853 { 854 "id": "pipeline23", 855 "name": "MOSHPIT", 856 "attributes": { 857 "qc": [ 858 "Cutadapt", 859 "Bowtie2" 860 ], 861 "assembly": [ 862 "SPAdes", 863 "MEGAHIT" 864 ], 865 "binning": [ 866 "MetaBAT2" 867 ], 868 "qualityAssessment": [ 869 "QUAST", 870 "BUSCO" 871 ], 872 "refinement": [ 873 "Sourmash" 874 ], 875 "taxonomy": [ 876 "Kraken2", 877 "Kaiju" 878 ], 879 "functionalAnnotation": [ 880 "eggNOG-mapper", 881 "DIAMOND (eggNOG, CAZy)" 882 ], 883 "other": [] 884 }, 885 "description": "MOSHPIT pipeline.", 886 "url": "", 887 "details": "", 888 "category": "Metagenomic MAG Reconstruction Pipelines" 889 }, 890 { 891 "id": "pipeline24", 892 "name": "MUFFIN", 893 "attributes": { 894 "qc": [ 895 "fastp", 896 "Filtlong" 897 ], 898 "assembly": [ 899 "SPAdes", 900 "Flye", 901 "Unicycler" 902 ], 903 "binning": [ 904 "MetaBAT2", 905 "CONCOCT", 906 "MaxBin2" 907 ], 908 "qualityAssessment": [
909 "CheckM" 910 ], 911 "refinement": [ 912 "MetaWRAP-native module" 913 ], 914 "taxonomy": [ 915 "Sourmash (GTDB)" 916 ], 917 "functionalAnnotation": [ 918 "eggNOG-mapper" 919 ], 920 "other": [ 921 "Salmon", 922 "Trinity" 923 ] 924 }, 925 "description": "MUFFIN pipeline.", 926 "url": "", 927 "details": "", 928 "category": "Metagenomic MAG Reconstruction Pipelines" 929 }, 930 { 931 "id": "pipeline25", 932 "name": "NanoPhase", 933 "attributes": { 934 "qc": [ 935 "Filtlong" 936 ], 937 "assembly": [ 938 "metaFlye", 939 "Racon", 940 "medaka" 941 ], 942 "binning": [ 943 "MetaBAT2", 944 "MaxBin2" 945 ], 946 "qualityAssessment": [ 947 "CheckM", 948 "QUAST" 949 ], 950 "refinement": [ 951 "MetaWRAP-native module" 952 ], 953 "taxonomy": [ 954 "GTDB-Tk" 955 ], 956 "functionalAnnotation": [ 957 "Prodigal", 958 "DIAMOND (UniProtKB)" 959 ], 960 "other": [] 961 }, 962 "description": "NanoPhase pipeline.", 963 "url": "", 964 "details": "", 965 "category": "Metagenomic MAG Reconstruction Pipelines" 966 }, 967 { 968 "id": "pipeline26", 969 "name": "nf-core/mag", 970 "attributes": { 971 "qc": [ 972 "fastp", 973 "AdapterRemoval", 974 "Bowtie2", 975 "BBTools", 976 "Trimmomatic", 977 "FastQC", 978 "Porechop", 979 "Filtlong", 980 "NanoPack2", 981 ], 982 "assembly": [ 983 "MEGAHIT", 984 "SPAdes", 985 "hybridSPAdes", 986 "Flye", 987 "metaMDBG" 988 ], 989 "binning": [ 990 "MetaBAT2", 991 "CONCOCT", 992 "MaxBin2" 993 ], 994 "qualityAssessment": [ 995 "BUSCO", 996 "CheckM", 997 "CheckM2", 998 "GUNC", 999 "QUAST" 1000 ], 1001 "refinement": [ 1002 "DASTool" 1003 ], 1004 "taxonomy": [ 1005 "GTDB-Tk2", 1006 "CAT" 1007 ], 1008 "functionalAnnotation": [ 1009 "Prodigal", 1010 "Prokka", 1011 "MetaEuk" 1012 ], 1013 "other": [ 1014 "Kraken2", 1015 "Centrifuge", 1016 "geNomad", 1017 "Tiara", 1018 "PyDamage", 1019 "MultiQC" 1020 ] 1021 }, 1022 "description": "nf-core/mag pipeline.", 1023 "url": "", 1024 "details": "", 1025 "category": "Metagenomic MAG Reconstruction Pipelines" 1026 }, 1027 { 1028 "id": "pipeline27", 1029 "name": "ngs-preprocess-MpGAP-Bacannot", 1030 "attributes": { 1031 "qc": [ 1032 "Porechop", 1033 "NanoPack2", 1034 "pycoQC", 1035 "fastp" 1036 ], 1037 "assembly": [ 1038 "SPAdes", 1039 "Flye", 1040 "Canu", 1041 "Unicycler", 1042 "Shovill", 1043 "HASLR", 1044 "Raven", 1045 "Shasta", 1046 "wtdbg2", 1047 "Pilon" 1048 ], 1049 "binning": [], 1050 "qualityAssessment": [], 1051 "refinement": [], 1052 "taxonomy": [], 1053 "functionalAnnotation": [ 1054 "Prokka", 1055 "KOfamScan", 1056 "KEGGDecoder", 1057 "Bakta", 1058 "Barrnap", 1059 "antiSMASH" 1060 ], 1061 "other": [ 1062 "AMRFinderPlus", 1063 "CARD-RGI", 1064 "BEDTools", 1065 "Phigaro", 1066 "VFDB", 1067 "PlasmidFinder", 1068 "MLST", 1069 "Platon", 1070 "PHASTER", 1071 "ARGminer", 1072 "ResFinder" 1073 ] 1074 }, 1075 "description": "ngs-preprocess-MpGAP-Bacannot pipeline.", 1076 "url": "", 1077 "details": "", 1078 "category": "Metagenomic MAG Reconstruction Pipelines" 1079 }, 1080 { 1081 "id": "pipeline28", 1082 "name": "SnakeMAGs", 1083 "attributes": { 1084 "qc": [ 1085 "Illumina-utils", 1086 "Trimmomatic", 1087 "Bowtie2" 1088 ], 1089 "assembly": [ 1090 "MEGAHIT" 1091 ], 1092 "binning": [ 1093 "MetaBAT2" 1094 ], 1095 "qualityAssessment": [ 1096 "CheckM", 1097 "GUNC", 1098 "CoverM" 1099 ], 1100 "refinement": [ 1101 1102 ], 1103 "taxonomy": ["GTDB-Tk2"], 1104 "functionalAnnotation": [], 1105 "other": [] 1106 }, 1107 "description": "SnakeMAGs pipeline.", 1108 "url": "", 1109 "details": "", 1110 "category": "Metagenomic MAG Reconstruction Pipelines" 1111 }, 1112 { 1113 "id": "pipeline29", 1114 "name": "SqueezeMeta", 1115 "attributes": { 1116 "qc": [ 1117 "PRINSEQ", 1118 "Trimmomatic", 1119 "SAMtools" 1120 ], 1121 "assembly": [ 1122 "MEGAHIT", 1123 "SPAdes", 1124 "Canu", 1125 "Flye" 1126 ], 1127 "binning": [ 1128 "MetaBAT2", 1129 "CONCOCT", 1130 "MaxBin2" 1131 ], 1132 "qualityAssessment": [ 1133 "CheckM", 1134 "CheckM2", 1135 "CompareM" 1136 ], 1137 "refinement": [ 1138 "DASTool" 1139 ], 1140 "taxonomy": [ 1141 "GTDB-Tk2" 1142 ], 1143 "functionalAnnotation": [ 1144 "Prodigal", 1145 "MUMmer", 1146 "HMMER", 1147 "Barrnap" 1148 ], 1149 "other": [ 1150 "POGENOM", 1151 "DIAMOND (NCBI COG, KEGG)", 1152 "SQMtools" 1153 ] 1154 }, 1155 "description": "SqueezeMeta pipeline.", 1156 "url": "", 1157 "details": "", 1158 "category": "Metagenomic MAG Reconstruction Pipelines" 1159 }, 1160 { 1161 "id": "pipeline30", 1162 "name": "Sunbeam", 1163 "attributes": { 1164 "qc": [ 1165 "Trimmomatic", 1166 "Cutadapt", 1167 "Komplexity", 1168 "BWA" 1169 ], 1170 "assembly": [ 1171 "MEGAHIT" 1172 ], 1173 "binning": [], 1174 "qualityAssessment": [], 1175 "refinement": [], 1176 "taxonomy": [], 1177 "functionalAnnotation": [ 1178 "Prodigal", 1179 "BLAST", 1180 "DIAMOND" 1181 ], 1182 "other": [ 1183 "Kraken" 1184 ] 1185 }, 1186 "description": "Sunbeam pipeline.", 1187 "url": "", 1188 "details": "", 1189 "category": "Metagenomic MAG Reconstruction Pipelines" 1190 }, 1191 { 1192 "id": "pipeline31", 1193 "name": "VEBA", 1194 "attributes": { 1195 "qc": [ 1196 "KneadData", 1197 "fastp", 1198 "BBTools", 1199 "Bowtie2", 1200 "NanoPack2", 1201 "Minimap2" 1202 ], 1203 "assembly": [ 1204 "metaSPAdes", 1205 "SPAdes", 1206 "rnaSPAdes", 1207 "MEGAHIT", 1208 "Flye", 1209 "metaFlye" 1210 ], 1211 "binning": [ 1212 "MetaBAT2", 1213 "CONCOCT", 1214 "MaxBin2", 1215 "SemiBin2" 1216 ], 1217 "qualityAssessment": [ 1218 "CheckM2", 1219 "Tiara", 1220 "CheckV", 1221 "BUSCO", 1222 "CoverM" 1223 ], 1224 "refinement": [ 1225 "Binette" 1226 ], 1227 "taxonomy": [ 1228 "GTDB-Tk2", 1229 "MetaEuk", 1230 "geNomad", 1231 "VirFinder" 1232 ], 1233 "functionalAnnotation": [ 1234 "Prodigal", 1235 "DIAMOND (UniRef50/90, MIBiG, VFDB, CAZy)", 1236 "HMMER (Pfam, NCBIfam-AMR, AntiFam, KOfamKOALA)", 1237 "MicrobeAnnotator" 1238 ], 1239 "other": [ 1240 "antiSMASH", 1241 "Muscle5", 1242 "FastTree2", 1243 "FastANI", 1244 "sylph", 1245 "HUMAnN3" 1246 ] 1247 }, 1248 "description": "VEBA pipeline.", 1249 "url": "", 1250 "details": "", 1251 "category": "Metagenomic MAG Reconstruction Pipelines" 1252 }, 1253 { 1254 "id": "pipeline32", 1255 "name": "BugBuster", 1256 "attributes": { 1257 "qc": [ 1258 "fastp", 1259 "Bowtie2" 1260 ], 1261 "assembly": [ 1262 "MEGAHIT" 1263 ], 1264 "binning": [ 1265 "MetaBAT2", 1266 "SemiBin2", 1267 "COMEBin" 1268 ], 1269 "qualityAssessment": [ 1270 "CheckM2" 1271 ], 1272 "refinement": [ 1273 "MetaWRAP-native module" 1274 ], 1275 "taxonomy": [ 1276 "GTDB-Tk2" 1277 ], 1278 "functionalAnnotation": [ 1279 "Prodigal", 1280 "MetaCerberus" 1281 ], 1282 "other": [ 1283 "deepARG", 1284 "Kraken2", 1285 "Sourmash" 1286 ] 1287 }, 1288 "description": "BugBuster pipeline.", 1289 "url": "", 1290 "details": "", 1291 "category": "Metagenomic MAG Reconstruction Pipelines" 1292 }, 1293 { 1294 "id": "pipeline33", 1295 "name": "MG-TK", 1296 "attributes": { 1297 "qc": [ 1298 "Trimmomatic", 1299 "Porechop", 1300 "Kraken", 1301 "Kraken2", 1302 "SDM" 1303 ], 1304 "assembly": [ 1305 "SPAdes", 1306 "MEGAHIT", 1307 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], 1366 "functionalAnnotation": [ 1367 "Prokka" 1368 ], 1369 "other": [ 1370 "Roary", 1371 "ezTree", 1372 "FastANI" 1373 ] 1374 }, 1375 "description": "MAGO pipeline.", 1376 "url": "", 1377 "details": "", 1378 "category": "Metagenomic MAG Reconstruction Pipelines" 1379 }, 1380 { 1381 "id": "pipeline35", 1382 "name": "IMG/M", 1383 "attributes": { 1384 "qc": [ 1385 1386 ], 1387 "assembly": [ 1388 1389 ], 1390 "binning": [ 1391 "SemiBin2" 1392 1393 ], 1394 "qualityAssessment": [ 1395 "CheckM" 1396 ], 1397 "refinement": [], 1398 "taxonomy": [ 1399 "GTDB-Tk" 1400 ], 1401 "functionalAnnotation": [ 1402 "Prodigal", 1403 "GeneMarkS-2", 1404 "HMMER (NCBI COG, Pfam, TIGRFAMs)" 1405 ], 1406 "other": [ 1407 "EukCC", 1408 "SignalP", 1409 "TMHMM" 1410 ] 1411 }, 1412 "description": "IMG/M pipeline.", 1413 "url": "", 1414 "details": "", 1415 "category": "Metagenomic MAG Reconstruction Pipelines" 1416 }, 1417 { 1418 "id": "pipeline36", 1419 "name": "WGSA2+/LoRA", 1420 "attributes": { 1421 "qc": [ 1422 "KneadData", 1423 "fastp", 1424 "Kraken2" 1425 1426 ], 1427 "assembly": [ 1428 "metaSPAdes", 1429 "metaFlye", 1430 "Minimap2", 1431 "Samtools" 1432 ], 1433 "binning": [ 1434 "MetaBAT2" 1435 1436 ], 1437 "qualityAssessment": [ 1438 "CheckM", 1439 "CheckM2" 1440 ], 1441 "refinement": [], 1442 "taxonomy": [ 1443 "GTDB-Tk2" 1444 ], 1445 "functionalAnnotation": [ 1446 "Prodigal", 1447 "eggNOG-mapper", 1448 "MinPath" 1449 ], 1450 "other": [ 1451 "SortMeRNA", 1452 "Krona", 1453 "Trinity" 1454 ] 1455 }, 1456 "description": "WGSA2+/LoRA pipeline.", 1457 "url": "", 1458 "details": "", 1459 "category": "Metagenomic MAG Reconstruction Pipelines" 1460 }, 1461 { 1462 "id": "pipeline37", 1463 "name": "JAMS", 1464 "attributes": { 1465 "qc": [ 1466 "Trimmomatic", 1467 "Bowtie2" 1468 1469 ], 1470 "assembly": [ 1471 "SPAdes", 1472 "MEGAHIT" 1473 ], 1474 "binning": [ 1475 1476 ], 1477 "qualityAssessment": [ 1478 1479 ], 1480 "refinement": [], 1481 "taxonomy": [ 1482 "Kraken2" 1483 ], 1484 "functionalAnnotation": [ 1485 "Prokka", 1486 "InterProScan" 1487 ], 1488 "other": [ 1489 "Samtools", 1490 "BEDTools", 1491 ] 1492 }, 1493 "description": "JAMS pipeline.", 1494 "url": "", 1495 "details": "", 1496 "category": "Metagenomic MAG Reconstruction Pipelines" 1497 }, 1498 { 1499 "id": "pipeline38", 1500 "name": "SPIRE", 1501 "attributes": { 1502 "qc": [ 1503 "NGLess" 1504 1505 ], 1506 "assembly": [ 1507 "MEGAHIT", 1508 "BWA", 1509 "Samtools" 1510 ], 1511 "binning": [ 1512 "MetaBAT2" 1513 ], 1514 "qualityAssessment": [ 1515 "CheckM2", 1516 "GUNC" 1517 1518 ], 1519 "refinement": [], 1520 "taxonomy": [ 1521 "GTDB-Tk2" 1522 ], 1523 "functionalAnnotation": [ 1524 "Prodigal", 1525 "eggNOG-mapper" 1526 ], 1527 "other": [ 1528 "Barrnap", 1529 "abricate (MEGARes, VFDB)", 1530 "Seqtk", 1531 "macrel", 1532 "Mash" 1533 ] 1534 }, 1535 "description": "SPIRE pipeline.", 1536 "url": "", 1537 "details": "", 1538 "category": "Metagenomic MAG Reconstruction Pipelines" 1539 }, 1540 { 1541 "id": "pipeline39", 1542 "name": "EURYALE (MEDUSA)", 1543 "attributes": { 1544 "qc": [ 1545 "FastQC", 1546 "fastp", 1547 "Bowtie2", 1548 "MultiQC" 1549 1550 ], 1551 "assembly": [ 1552 "MEGAHIT", 1553 ], 1554 "binning": [ 1555 1556 ], 1557 "qualityAssessment": [ 1558 1559 ], 1560 "refinement": [], 1561 "taxonomy": [ 1562 "Kaiju", 1563 "Kraken2" 1564 ], 1565 "functionalAnnotation": [ 1566 "DIAMOND (NCBI nr)" 1567 ], 1568 "other": [ 1569 "Krona" 1570 ] 1571 }, 1572 "description
1572": "EURYALE (MEDUSA) pipeline.", 1573 "url": "", 1574 "details": "", 1575 "category": "Metagenomic MAG Reconstruction Pipelines" 1576 }, 1577 { 1578 "id": "pipeline40", 1579 "name": "nIMP3", 1580 "attributes": { 1581 "qc": [ 1582 "BWA", 1583 "Samtools", 1584 "BBTools", 1585 "FastQC", 1586 "SortMeRNA" 1587 ], 1588 "assembly": [ 1589 "MEGAHIT", 1590 ], 1591 "binning": [ 1592 1593 ], 1594 "qualityAssessment": [ 1595 1596 ], 1597 "refinement": [], 1598 "taxonomy": [ 1599 "Kraken2" 1600 ], 1601 "functionalAnnotation": [ 1602 "gffquant" 1603 ], 1604 "other": [ 1605 "mOTUs", 1606 "MultiQC", 1607 "MetaPhlAn4", 1608 "Salmon", 1609 "kallisto" 1610 ] 1611 }, 1612 "description": "nIMP3 pipeline.", 1613 "url": "", 1614 "details": "", 1615 "category": "Metagenomic MAG Reconstruction Pipelines" 1616 }, 1617 { 1618 "id": "pipeline41", 1619 "name": "Mapler", 1620 "attributes": { 1621 "qc": [ 1622 "FastQC" 1623 ], 1624 "assembly": [ 1625 "metaMDBG", 1626 "metaFlye", 1627 "hifiasm", 1628 "OPERA-MS", 1629 "Minimap2" 1630 ], 1631 "binning": [ 1632 "MetaBAT2" 1633 ], 1634 "qualityAssessment": [ 1635 "CheckM2", 1636 "metaQUAST" 1637 ], 1638 "refinement": [], 1639 "taxonomy": [ 1640 "Kraken2", 1641 "GTDB-Tk2" 1642 ], 1643 "functionalAnnotation": [ 1644 1645 ], 1646 "other": [ 1647 "KAT" 1648 ] 1649 }, 1650 "description": "Mapler pipeline.", 1651 "url": "", 1652 "details": "", 1653 "category": "Metagenomic MAG Reconstruction Pipelines" 1654 }, 1655 { 1656 "id": "pipeline42", 1657 "name": "ont-assembly-snake/score-assemblies", 1658 "attributes": { 1659 "qc": [ 1660 "Filtlong", 1661 "Rasusa" 1662 ], 1663 "assembly": [ 1664 "Raven", 1665 "Flye", 1666 "Miniasm", 1667 "Canu", 1668 "Unicycler", 1669 "Racon", 1670 "medaka", 1671 "Pilon", 1672 "Polypolish", 1673 "POLCA" 1674 ], 1675 "binning": [ 1676 1677 ], 1678 "qualityAssessment": [ 1679 "QUAST", 1680 "BUSCO", 1681 "DNAdiff (MUMmer)", 1682 "Pomoxis" 1683 ], 1684 "refinement": [], 1685 "taxonomy": [ 1686 1687 ], 1688 "functionalAnnotation": [ 1689 "Prodigal", 1690 "Bakta", 1691 "DIAMOND (SwissProt)" 1692 ], 1693 "other": [ 1694 "Homopolish", 1695 "Proovframe" 1696 ] 1697 }, 1698 "description": "ont-assembly-snake/score-assemblies pipeline.", 1699 "url": "", 1700 "details": "", 1701 "category": "Metagenomic MAG Reconstruction Pipelines" 1702 }, 1703 { 1704 "id": "pipeline43", 1705 "name": "Bactopia", 1706 "attributes": { 1707 "qc": [ 1708 "BBTools", 1709 "fastp", 1710 "FastQC", 1711 "NanoPack2", 1712 "Rasusa", 1713 "Porechop", 1714 "fastq-scan" 1715 ], 1716 "assembly": [ 1717 "Shovill", 1718 "Dragonflye", 1719 "Unicycler" 1720 ], 1721 "binning": [ 1722 1723 ], 1724 "qualityAssessment": [ 1725 "CheckM", 1726 "QUAST", 1727 "BUSCO" 1728 ], 1729 "refinement": [], 1730 "taxonomy": [ 1731 "GTDB-Tk2" 1732 ], 1733 "functionalAnnotation": [ 1734 "Bakta", 1735 "Prokka" 1736 ], 1737 "other": [ 1738 "Merlin", 1739 "Sourmash", 1740 "Mash", 1741 "MLST", 1742 "AMRFinderPlus", 1743 "Kraken2", 1744 "Bracken", 1745 "FastANI" 1746 ] 1747 }, 1748 "description": "Bactopia pipeline.", 1749 "url": "", 1750 "details": "", 1751 "category": "Metagenomic MAG Reconstruction Pipelines" 1752 }, 1753 { 1754 "id": "pipeline44", 1755 "name": "Arcadia-Science/metagenomics", 1756 "attributes": { 1757 "qc": [ 1758 "fastp", 1759 "NanoPack2", 1760 "Porechop", 1761 ], 1762 "assembly": [ 1763 "metaSPAdes", 1764 "Flye", 1765 "medaka" 1766 ], 1767 "binning": [ 1768 1769 ], 1770 "qualityAssessment": [ 1771 "QUAST" 1772 ], 1773 "refinement": [], 1774 "taxonomy": [
1775 "Sourmash (user-provided database)" 1776 ], 1777 "functionalAnnotation": [ 1778 "Prodigal", 1779 "DIAMOND (user-provided database)" 1780 ], 1781 "other": [ 1782 "Bowtie2", 1783 "Minimap2" 1784 ] 1785 }, 1786 "description": "Arcadia-Science/metagenomics pipeline.", 1787 "url": "", 1788 "details": "", 1789 "category": "Metagenomic MAG Reconstruction Pipelines" 1790 }, 1791 { 1792 "id": "pipeline45", 1793 "name": "baargin", 1794 "attributes": { 1795 "qc": [ 1796 "fastp" 1797 ], 1798 "assembly": [ 1799 "SPAdes", 1800 "Unicycler" 1801 ], 1802 "binning": [ 1803 ], 1804 "qualityAssessment": [ 1805 "QUAST", 1806 "BUSCO" 1807 ], 1808 "refinement": [], 1809 "taxonomy": [ 1810 "Kraken2" 1811 ], 1812 "functionalAnnotation": [ 1813 "Prokka", 1814 "Bakta" 1815 ], 1816 "other": [ 1817 "AMRFinderPlus", 1818 "CARD-RGI", 1819 "PlasmidFinder", 1820 "MLST", 1821 "Platon", 1822 "Roary" 1823 ] 1824 }, 1825 "description": "baargin", 1826 "url": "", 1827 "details": "", 1828 "category": "Metagenomic MAG Reconstruction Pipelines" 1829 }, 1830 { 1831 "id": "pipeline46", 1832 "name": "nf-core/metatdenovo", 1833 "attributes": { 1834 "qc": [ 1835 "TrimGalore", 1836 "BBTools", 1837 "Seqtk" 1838 ], 1839 "assembly": [ 1840 "rnaSPAdes", 1841 "MEGAHIT" 1842 ], 1843 "binning": [ 1844 ], 1845 "qualityAssessment": [ 1846 ], 1847 "refinement": [], 1848 "taxonomy": [ 1849 "EUKulele", 1850 "DIAMOND (user-provided database)" 1851 ], 1852 "functionalAnnotation": [ 1853 "TransDecoder", 1854 "Prodigal", 1855 "Prokka", 1856 "Bakta", 1857 "eggNOG-mapper", 1858 "HMMER", 1859 ], 1860 "other": [ 1861 "MultiQC", 1862 ] 1863 }, 1864 "description": "nf-core/metatdenovo", 1865 "url": "", 1866 "details": "", 1867 "category": "Metagenomic MAG Reconstruction Pipelines" 1868 }, 1869 { 1870 "id": "pipeline47", 1871 "name": "mmlong2", 1872 "attributes": { 1873 "qc": [ 1874 1875 ], 1876 "assembly": [ 1877 "metaFlye", 1878 "medaka", 1879 ], 1880 "binning": [ 1881 "VAMB", 1882 "SemiBin2", 1883 "MetaBAT2", 1884 "COMEBin", 1885 ], 1886 "qualityAssessment": [ 1887 "CheckM2", 1888 "CheckM", 1889 "GUNC", 1890 "QUAST", 1891 "CoverM" 1892 ], 1893 "refinement": [ 1894 "Binette" 1895 ], 1896 "taxonomy": [ 1897 "GTDB-Tk", 1898 "Metabuli" 1899 ], 1900 "functionalAnnotation": [ 1901 "Bakta" 1902 ], 1903 "other": [ 1904 "Cramino", 1905 "Jellyfish", 1906 "Tiara", 1907 "Longshot", 1908 "NanoQ", 1909 "USEARCH" 1910 ] 1911 }, 1912 "description": "mmlong2", 1913 "url": "", 1914 "details": "", 1915 "category": "Metagenomic MAG Reconstruction Pipelines" 1916 }, 1917 { 1918 "id": "pipeline48", 1919 "name": "MetaMAG", 1920 "attributes": { 1921 "qc": [ 1922 "FastQC", 1923 "fastp", 1924 "BWA", 1925 "Samtools" 1926 ], 1927 "assembly": [ 1928 "IDBA-UD", 1929 "MEGAHIT", 1930 ], 1931 "binning": [ 1932 "MetaBAT2", 1933 "MaxBin2", 1934 "CONCOCT", 1935 ], 1936 "qualityAssessment": [ 1937 "CheckM2", 1938 ], 1939 "refinement": [ 1940 "DASTool", 1941 ], 1942 "taxonomy": [ 1943 "GTDB-Tk2", 1944 "Metabuli" 1945 ], 1946 "functionalAnnotation": [ 1947 "eggNOG-mapper", 1948 "dbCAN3", 1949 "Prodigal" 1950 ], 1951 "other": [ 1952 "dRep", 1953 "FastANI", 1954 "Kraken2" 1955 ] 1956 }, 1957 "description": "MetaMAG", 1958 "url": "", 1959 "details": "", 1960 "category": "Metagenomic MAG Reconstruction Pipelines" 1961 }, 1962 { 1963 "id": "pipeline49", 1964 "name": "MAGFlow", 1965 "attributes": { 1966 "qc": [ 1967 "Sickle", 1968 ], 1969 "assembly": [ 1970 "metaSPAdes", 1971 ], 1972 "binning": [ 1973 "MetaBAT2", 1974 "MaxBin2", 1975 "CONCOCT", 1976 ], 1977 "qualityAssessment": [ 1978 "CheckM", 1979 ], 1980 "refinement": [ 1981 "DASTool", 1982 ], 1983 "taxonomy": [ 1984 1985 ], 1986 "functionalAnnotation": [ 1987 1988 ], 1989 "other": [ 1990 "Bowtie2", 1991 ] 1992 }, 1993 "description": "MAGFlow", 1994 "url": "", 1995 "details": "", 1996 "category": "Metagenomic MAG Reconstruction Pipelines" 1997 }, 1998 { 1999 "id": "pipeline50", 2000 "name": "metaFUN", 2001 "attributes": { 2002 "qc": [ 2003 "FastQC", 2004 "fastp", 2005 "MultiQC", 2006 "Bowtie2" 2007 ], 2008 "assembly": [ 2009 "MEGAHIT", 2010 ], 2011 "binning": [ 2012 "MetaBAT2", 2013 "SemiBin2", 2014 ], 2015 "qualityAssessment": [ 2016 "CheckM2", 2017 "GUNC" 2018 ], 2019 "refinement": [ 2020 "DASTool", 2021 ], 2022 "taxonomy": [ 2023 "GTDB-Tk2" 2024 ], 2025 "functionalAnnotation": [ 2026 "Prokka", 2027 "KOfamScan", 2028 "eggNOG-mapper", 2029 "dbCAN3", 2030 "DIAMOND (VFDB)" 2031 ], 2032 "other": [ 2033 "skani", 2034 "HUMAnN3", 2035 "inStrain", 2036 "Kraken2", 2037 "Bracken", 2038 "sylph", 2039 "CARD-RGI" 2040 ] 2041 }, 2042 "description": "metaFUN", 2043 "url": "", 2044 "details": "", 2045 "category": "Metagenomic MAG Reconstruction Pipelines" 2046 }, 2047]; 2048 2049// Expose globally for non-module usage in index.html 2050window.MAG_PIPELINES_XLSX = MAG_PIPELINES;
Line numbers count LF bytes from the start of the resource, as the search results do. Vendor segments are library code the classifier recognised; they are stored but not indexed. Bytes are shown as Latin1 characters, one per byte.