Mercurial > repos > youyuh48 > combine_bracken_outputs
view test-data/sample1_output_species_abundance.txt @ 0:6e90a30b214f draft default tip
planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
| author | youyuh48 |
|---|---|
| date | Sun, 14 Jul 2024 08:45:50 +0000 |
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| children |
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name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads Streptococcus sanguinis 1305 S 21 0 21 0.00000 Streptococcus suis 1307 S 22 1 23 0.00000 Streptococcus gordonii 1302 S 10 0 10 0.00000 Vibrio cholerae 666 S 10 4 14 0.00000 Bacillus methylotrophicus 492670 S 23 0 23 0.00000 Streptococcus thermophilus 1308 S 34 0 34 0.00000 Streptococcus mutans 1309 S 10 0 10 0.00000 Burkholderia xenovorans 36873 S 34 0 34 0.00000 Sinorhizobium medicae 110321 S 54 0 54 0.00000 Burkholderia phymatum 148447 S 655478 1228 656706 0.02503 Borrelia burgdorferi 139 S 36 0 36 0.00000 Nostoc punctiforme 272131 S 590086 562 590648 0.02251 Shewanella frigidimarina 56812 S 23 0 23 0.00000 Clostridium novyi 1542 S 211808 388 212196 0.00809 Mycobacterium tuberculosis 1773 S 20647 274350 294997 0.01124 Mycobacterium smegmatis 1772 S 239 0 239 0.00001 Rhodopseudomonas palustris 1076 S 823190 1106 824296 0.03141 Bacteroides thetaiotaomicron 818 S 392179 3490 395669 0.01508 Mycobacterium abscessus 36809 S 78 0 78 0.00000 Burkholderia multivorans 87883 S 30 5 35 0.00000 Citrobacter koseri 545 S 576 17 593 0.00002 Bordetella pertussis 520 S 632 732 1364 0.00005 Chlamydia trachomatis 813 S 71933 284 72217 0.00275 Pseudomonas aeruginosa 287 S 42 1 43 0.00000 Chlamydia pneumoniae 83558 S 78615 83 78698 0.00300 Haloquadratum walsbyi 293091 S 223986 31 224017 0.00854 Streptococcus pyogenes 1314 S 252007 4976 256983 0.00979 Streptococcus pneumoniae 1313 S 177347 1168 178515 0.00680 Pelodictyon luteolum 1100 S 157283 1662 158945 0.00606 Streptococcus agalactiae 1311 S 159789 4251 164040 0.00625 Pseudomonas protegens 380021 S 18 0 18 0.00000 Salmonella enterica 28901 S 387186 4916 392102 0.01494 Francisella tularensis 263 S 120338 554 120892 0.00461 Clostridium botulinum 1491 S 281791 594 282385 0.01076 Alkaliphilus metalliredigens 208226 S 368065 432 368497 0.01404 Shewanella denitrificans 192073 S 17 0 17 0.00000 Shewanella sp. MR-7 60481 S 224465 86579 311044 0.01185 Bacillus licheniformis 1402 S 13 0 13 0.00000 Burkholderia ambifaria 152480 S 27 3 30 0.00000 Alkalilimnicola ehrlichii 351052 S 226337 74 226411 0.00863 Corynebacterium jeikeium 38289 S 20 0 20 0.00000 Pediococcus pentosaceus 1255 S 13 0 13 0.00000 Bacillus anthracis 1392 S 151306 277437 428743 0.01634 Hyphomonas neptunium 81032 S 262956 33 262989 0.01002 Borrelia afzelii 29518 S 37 0 37 0.00000 Pseudomonas fluorescens 294 S 21 1 22 0.00000 Corynebacterium urealyticum 43771 S 168078 3426 171504 0.00654 Bacillus clausii 79880 S 281618 346 281964 0.01075 Campylobacter concisus 199 S 157661 329 157990 0.00602 Shewanella baltica 62322 S 108 1 109 0.00000 Pseudomonas stutzeri 316 S 293151 1980 295131 0.01125 Cytophaga hutchinsonii 985 S 307508 31 307539 0.01172 Cyanothece sp. ATCC 51142 43989 S 372257 54 372311 0.01419 Thermus thermophilus 274 S 152701 13 152714 0.00582 Bacillus cytotoxicus 580165 S 643 5 648 0.00002 Clostridium acetobutylicum 1488 S 13 0 13 0.00000 Burkholderia cenocepacia 95486 S 29 50 79 0.00000 Corynebacterium efficiens 152794 S 233423 670 234093 0.00892 Chromobacterium violaceum 536 S 330985 434 331419 0.01263 Ureaplasma parvum 134821 S 47612 5 47617 0.00181 Bacillus pumilus 1408 S 20 0 20 0.00000 Enterobacter sp. 638 399742 S 290 1 291 0.00001 Bordetella avium 521 S 81 0 81 0.00000 Bacillus cereus 1396 S 1086754 202070 1288824 0.04912 Ochrobactrum anthropi 529 S 381841 1054 382895 0.01459 Thermosipho melanesiensis 46541 S 128132 53 128185 0.00489 Mycobacterium marinum 1781 S 281340 152004 433344 0.01651 Nostoc sp. PCC 7120 103690 S 247 7 254 0.00001 Pseudomonas mendocina 300 S 14 1 15 0.00000 Lactococcus lactis 1358 S 404921 2772 407693 0.01554 Pseudomonas putida 303 S 511201 4777 515978 0.01966 Sinorhizobium meliloti 382 S 420783 3928 424711 0.01619 Clostridium beijerinckii 1520 S 418932 1011 419943 0.01600 Geobacillus thermodenitrificans 33940 S 11 11 22 0.00000 Saccharopolyspora erythraea 1836 S 10 0 10 0.00000 Shewanella oneidensis 70863 S 222 4 226 0.00001 Bradyrhizobium sp. ORS 278 114615 S 14 5 19 0.00000 Rickettsia typhi 785 S 43 0 43 0.00000 Methanococcus maripaludis 39152 S 121232 302 121534 0.00463 Rickettsia prowazekii 782 S 70541 1619 72160 0.00275 Listeria innocua 1642 S 33 1 34 0.00000 Bordetella petrii 94624 S 233 5 238 0.00001 Bradyrhizobium diazoefficiens 1355477 S 17 0 17 0.00000 Mycobacterium sp. KMS 189918 S 11 267 278 0.00001 Bordetella parapertussis 519 S 348 1146 1494 0.00006 Bordetella bronchiseptica 518 S 128479 327016 455495 0.01736 Staphylococcus saprophyticus 29385 S 34 0 34 0.00000 Listeria monocytogenes 1639 S 43 1 44 0.00000 Cupriavidus taiwanensis 164546 S 12 0 12 0.00000 Chlamydophila caviae 83557 S 74403 340 74743 0.00285 Candidatus Blochmannia pennsylvanicus 101534 S 52480 50 52530 0.00200 Shigella flexneri 623 S 1022 4135 5157 0.00020 Shigella dysenteriae 622 S 1206 1447 2653 0.00010 Shigella boydii 621 S 1035 3475 4510 0.00017 Rhodococcus jostii 132919 S 622004 310 622314 0.02372 Shigella sonnei 624 S 605 1923 2528 0.00010 Klebsiella pneumoniae 573 S 333 5 338 0.00001 Sodalis glossinidius 63612 S 292996 614 293610 0.01119 Nitrosococcus oceani 1229 S 13 0 13 0.00000 Shewanella sp. MR-4 60480 S 336 137 473 0.00002 Neisseria meningitidis 487 S 143635 11544 155179 0.00591 Herpetosiphon aurantiacus 65 S 427279 27 427306 0.01628 Leptospira borgpetersenii 174 S 242592 345 242937 0.00926 Leptospira interrogans 173 S 13 0 13 0.00000 Photobacterium profundum 74109 S 12 1 13 0.00000 Lysinibacillus sphaericus 1421 S 47 0 47 0.00000 Clostridium perfringens 1502 S 17 0 17 0.00000 Bacillus subtilis 1423 S 265462 2267 267729 0.01020 Lawsonia intracellularis 29546 S 114759 23 114782 0.00437 Lactobacillus casei 1582 S 11 0 11 0.00000 Bacillus thuringiensis 1428 S 187882 159705 347587 0.01325 Psychrobacter arcticus 334543 S 78 0 78 0.00000 Oceanobacillus iheyensis 182710 S 15 0 15 0.00000 Lactobacillus helveticus 1587 S 12 0 12 0.00000 Lactobacillus delbrueckii 1584 S 153860 3163 157023 0.00598 Histophilus somni 731 S 136275 317 136592 0.00521 Wigglesworthia glossinidia 51229 S 66219 57 66276 0.00253 Cronobacter sakazakii 28141 S 270 3 273 0.00001 Yersinia enterocolitica 630 S 101 0 101 0.00000 Bacillus halodurans 86665 S 269485 450 269935 0.01029 Yersinia pestis 632 S 61383 252873 314256 0.01198 Burkholderia vietnamiensis 60552 S 26 5 31 0.00000 Photorhabdus luminescens 29488 S 51 0 51 0.00000 Bacillus weihenstephanensis 86662 S 1934 51 1985 0.00008 Idiomarina loihiensis 135577 S 187227 435 187662 0.00715 Prochlorococcus marinus 1219 S 307019 266 307285 0.01171 Ignicoccus hospitalis 160233 S 87443 14 87457 0.00333 Burkholderia lata 482957 S 16 2 18 0.00000 Lactobacillus salivarius 1624 S 139242 326 139568 0.00532 Syntrophomonas wolfei 863 S 193716 30 193746 0.00738 Burkholderia thailandensis 57975 S 1133 49 1182 0.00005 Haemophilus influenzae 727 S 117883 629 118512 0.00452 Cupriavidus necator 106590 S 29061 136 29197 0.00111 Acinetobacter sp. ADP1 62977 S 11 0 11 0.00000 Ruminiclostridium thermocellum 1515 S 260096 100 260196 0.00992 Erwinia tasmaniensis 338565 S 322076 1182 323258 0.01232 Clostridium tetani 1513 S 16 0 16 0.00000 Psychrobacter cryohalolentis 330922 S 413504 4426 417930 0.01593 Borrelia bavariensis 664662 S 78122 1938 80060 0.00305 Shewanella loihica 359303 S 10 0 10 0.00000 Pasteurella multocida 747 S 12 0 12 0.00000 Treponema denticola 158 S 183744 23 183767 0.00700 Yersinia pseudotuberculosis 633 S 709 1324 2033 0.00008 Pseudomonas entomophila 312306 S 52 0 52 0.00000 Halorhodospira halophila 1053 S 11 0 11 0.00000 Lachnoclostridium phytofermentans 66219 S 10 0 10 0.00000 Buchnera aphidicola 9 S 26192 14 26206 0.00100 Escherichia coli 562 S 717629 732184 1449813 0.05525 Coxiella burnetii 777 S 135506 22 135528 0.00516 Geobacter sulfurreducens 35554 S 244079 217 244296 0.00931 Anabaena variabilis 1172 S 433603 12868 446471 0.01701 Synechococcus elongatus 32046 S 466278 215 466493 0.01778 Serratia proteamaculans 28151 S 117 0 117 0.00000 Burkholderia pseudomallei 28450 S 224374 228836 453210 0.01727 Neisseria gonorrhoeae 485 S 135601 16923 152524 0.00581 Thiobacillus denitrificans 36861 S 226889 122 227011 0.00865 Burkholderia mallei 13373 S 193 3075 3268 0.00012 Pectobacterium atrosepticum 29471 S 96 0 96 0.00000 Listeria welshimeri 1643 S 176044 4791 180835 0.00689 Mycobacterium gilvum 1804 S 236 8 244 0.00001 Mycobacterium sp. JLS 164757 S 326114 373821 699935 0.02667 Staphylococcus aureus 1280 S 1192940 19301 1212241 0.04620 Staphylococcus haemolyticus 1283 S 33 0 33 0.00000 Staphylococcus epidermidis 1282 S 53 2 55 0.00000 Psychromonas ingrahamii 357794 S 287498 273 287771 0.01097 Shewanella amazonensis 60478 S 18 0 18 0.00000 Mycobacterium vanbaalenii 110539 S 244 4 248 0.00001 Shewanella sediminis 271097 S 12 0 12 0.00000 Acinetobacter baumannii 470 S 257301 727 258028 0.00983 Mycobacterium leprae 1769 S 31 0 31 0.00000 Mycobacterium bovis 1765 S 15035 264359 279394 0.01065 Mycobacterium ulcerans 1809 S 525 376 901 0.00003 Vibrio campbellii 680 S 11 3 14 0.00000 Mycobacterium avium 1764 S 310855 356 311211 0.01186 Shewanella sp. ANA-3 94122 S 405 42 447 0.00002