Mercurial > repos > iuc > krakentools_extract_kraken_reads
view test-data/3.tabular @ 2:4bf1e2701504 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 60eb96ad3ff782075ca1f29e26ffe5487bbb93ed
| author | iuc |
|---|---|
| date | Fri, 22 Nov 2024 09:28:12 +0000 |
| parents | 519e0835abd7 |
| children |
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name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads Enterococcus faecium 1352 S 19117311 5606915 24724226 0.91976 Enterococcus avium 33945 S 185099 8604 193703 0.00721 Enterococcus faecalis 1351 S 23719 2158 25877 0.00096 Enterococcus durans 53345 S 21563 1616 23179 0.00086 Enterococcus hirae 1354 S 18570 853 19423 0.00072 Enterococcus lactis 357441 S 14452 35311 49763 0.00185 Enterococcus mundtii 53346 S 13586 228 13814 0.00051 Enterococcus casseliflavus 37734 S 11263 3466 14729 0.00055 Enterococcus sp. FDAARGOS_375 2060307 S 5363 6531 11894 0.00044 Enterococcus sp. DA9 2603296 S 3725 15804 19529 0.00073 Enterococcus sp. FDAARGOS_553 2420313 S 339 1348 1687 0.00006 Enterococcus sp. M190262 2582830 S 162 175 337 0.00001 Enterococcus sp. CR-Ec1 2057791 S 58 52 110 0.00000 Enterococcus thailandicus 417368 S 5457 126 5583 0.00021 Enterococcus cecorum 44008 S 2805 68 2873 0.00011 Enterococcus saigonensis 1805431 S 2378 312 2690 0.00010 Enterococcus rotai 118060 S 1300 3 1303 0.00005 Enterococcus raffinosus 71452 S 1102 0 1102 0.00004 Enterococcus gilvus 160453 S 246 8 254 0.00001 Enterococcus gallinarum 1353 S 190 300 490 0.00002 Enterococcus wangshanyuanii 2005703 S 147 0 147 0.00001 Enterococcus innesii 2839759 S 72 0 72 0.00000 Vagococcus carniphilus 218144 S 693 52 745 0.00003 Vagococcus fluvialis 2738 S 281 0 281 0.00001 Vagococcus penaei 633807 S 62 1 63 0.00000 Vagococcus teuberi 519472 S 52 1 53 0.00000 Vagococcus lutrae 81947 S 33 0 33 0.00000 Vagococcus xieshaowenii 2562451 S 25 3 28 0.00000 Vagococcus zengguangii 2571750 S 24 2 26 0.00000 Vagococcus coleopterorum 2714946 S 12 0 12 0.00000 Tetragenococcus koreensis 290335 S 423 44 467 0.00002 Tetragenococcus halophilus 51669 S 82 10 92 0.00000 Tetragenococcus osmophilus 526944 S 52 14 66 0.00000 Melissococcus plutonius 33970 S 13 0 13 0.00000 Streptococcus thermophilus 1308 S 91845 3570 95415 0.00355 Streptococcus pyogenes 1314 S 2298 203 2501 0.00009 Streptococcus suis 1307 S 1790 39 1829 0.00007 Streptococcus agalactiae 1311 S 1315 1759 3074 0.00011 Streptococcus cristatus 45634 S 772 702 1474 0.00005 Streptococcus parauberis 1348 S 174 7 181 0.00001 Streptococcus pneumoniae 1313 S 156 159 315 0.00001 Streptococcus salivarius 1304 S 96 7 103 0.00000 Streptococcus infantis 68892 S 93 113 206 0.00001 Streptococcus sp. HSISS2 1316411 S 16 1 17 0.00000 Streptococcus sp. DAT741 1940319 S 16 2 18 0.00000 Streptococcus sp. HSISS3 1316412 S 11 1 12 0.00000 Streptococcus dysgalactiae 1334 S 47 17 64 0.00000 Streptococcus equi 1336 S 12 0 12 0.00000 Streptococcus gallolyticus 315405 S 54 7 61 0.00000 Streptococcus anginosus 1328 S 25 4 29 0.00000 Streptococcus constellatus 76860 S 16 103 119 0.00000 Streptococcus mitis 28037 S 42 1 43 0.00000 Streptococcus lutetiensis 150055 S 39 18 57 0.00000 Streptococcus pluranimalium 82348 S 30 0 30 0.00000 Streptococcus gordonii 1302 S 24 0 24 0.00000 Streptococcus vestibularis 1343 S 22 0 22 0.00000 Streptococcus pasteurianus 197614 S 20 18 38 0.00000 Streptococcus iniae 1346 S 20 0 20 0.00000 Streptococcus oralis 1303 S 17 0 17 0.00000 Streptococcus parasuis 1501662 S 16 0 16 0.00000 Streptococcus mutans 1309 S 11 0 11 0.00000 Streptococcus equinus 1335 S 10 0 10 0.00000 Lactococcus lactis 1358 S 554 571 1125 0.00004 Lactococcus raffinolactis 1366 S 255 9 264 0.00001 Lactococcus cremoris 1359 S 253 85 338 0.00001 Lactococcus garvieae 1363 S 223 40 263 0.00001 Lactococcus piscium 1364 S 22 18 40 0.00000 Lactococcus taiwanensis 1151742 S 16 0 16 0.00000 Lactococcus sp. LG606 2816912 S 10 9 19 0.00000 Jeotgalibaca sp. PTS2502 1903686 S 3404 392 3796 0.00014 Jeotgalibaca arthritidis 1868794 S 59 7 66 0.00000 Jeotgalibaca ciconiae 2496265 S 27 0 27 0.00000 Jeotgalibaca porci 1868793 S 25 1 26 0.00000 Granulicatella adiacens 46124 S 1042 0 1042 0.00004 Granulicatella elegans 137732 S 46 0 46 0.00000 Carnobacterium viridans 174587 S 93 0 93 0.00000 Carnobacterium maltaromaticum 2751 S 63 14 77 0.00000 Carnobacterium divergens 2748 S 56 5 61 0.00000 Carnobacterium inhibens 147709 S 24 6 30 0.00000 Marinilactibacillus sp. 15R 1911586 S 50 1 51 0.00000 Dolosigranulum pigrum 29394 S 17 0 17 0.00000 Limosilactobacillus vaginalis 1633 S 831 20 851 0.00003 Limosilactobacillus reuteri 1598 S 704 22 726 0.00003 Limosilactobacillus fermentum 1613 S 73 10 83 0.00000 Leuconostoc gelidum 1244 S 866 0 866 0.00003 Leuconostoc citreum 33964 S 37 23 60 0.00000 Leuconostoc lactis 1246 S 25 3 28 0.00000 Lactobacillus sp. wkB8 1545702 S 302 8 310 0.00001 Lactobacillus delbrueckii 1584 S 276 4 280 0.00001 Lactobacillus acidophilus 1579 S 43 19 62 0.00000 Lactobacillus jensenii 109790 S 18 1 19 0.00000 Lactobacillus iners 147802 S 17 0 17 0.00000 Lactobacillus johnsonii 33959 S 16 0 16 0.00000 Lactobacillus amylovorus 1604 S 14 0 14 0.00000 Lactobacillus acetotolerans 1600 S 12 0 12 0.00000 Lactobacillus helveticus 1587 S 10 0 10 0.00000 Weissella cibaria 137591 S 121 10 131 0.00000 Weissella jogaejeotgali 1631871 S 84 10 94 0.00000 Weissella hellenica 46256 S 18 1 19 0.00000 Weissella confusa 1583 S 15 1 16 0.00000 Ligilactobacillus salivarius 1624 S 153 4 157 0.00001 Ligilactobacillus murinus 1622 S 64 4 68 0.00000 Ligilactobacillus ruminis 1623 S 15 0 15 0.00000 Ligilactobacillus agilis 1601 S 14 0 14 0.00000 Lactiplantibacillus plantarum 1590 S 137 200 337 0.00001 Lactiplantibacillus paraplantarum 60520 S 11 0 11 0.00000 Pediococcus acidilactici 1254 S 68 2 70 0.00000 Pediococcus pentosaceus 1255 S 24 1 25 0.00000 Pediococcus damnosus 51663 S 11 1 12 0.00000 Latilactobacillus curvatus 28038 S 51 2 53 0.00000 Latilactobacillus sakei 1599 S 47 3 50 0.00000 Lacticaseibacillus paracasei 1597 S 34 17 51 0.00000 Levilactobacillus brevis 1580 S 35 3 38 0.00000 Periweissella cryptocerci 2506420 S 29 0 29 0.00000 Fructilactobacillus sanfranciscensis 1625 S 15 0 15 0.00000 Loigolactobacillus coryniformis 1610 S 10 2 12 0.00000 Acetilactobacillus jinshanensis 1720083 S 12 0 12 0.00000 Ignavigranum ruoffiae 89093 S 1065 0 1065 0.00004 Aerococcus urinaeequi 51665 S 137 19 156 0.00001 Aerococcus viridans 1377 S 89 22 111 0.00000 Suicoccus acidiformans 2036206 S 10 0 10 0.00000 Staphylococcus aureus 1280 S 12774 12776 25550 0.00095 Staphylococcus pseudintermedius 283734 S 1516 42 1558 0.00006 Staphylococcus warneri 1292 S 176 16 192 0.00001 Staphylococcus haemolyticus 1283 S 102 3 105 0.00000 Staphylococcus epidermidis 1282 S 51 1 52 0.00000 Staphylococcus argenteus 985002 S 13 5 18 0.00000 Staphylococcus hominis 1290 S 13 0 13 0.00000 Staphylococcus xylosus 1288 S 11 0 11 0.00000 Nosocomiicoccus ampullae 489910 S 143 0 143 0.00001 Mammaliicoccus sciuri 1296 S 65 3 68 0.00000 Mammaliicoccus vitulinus 71237 S 11 0 11 0.00000 Abyssicoccus albus 1817405 S 33 0 33 0.00000 Bacillus subtilis 1423 S 5091 4934 10025 0.00037 Bacillus velezensis 492670 S 210 43 253 0.00001 Bacillus amyloliquefaciens 1390 S 63 90 153 0.00001 Bacillus licheniformis 1402 S 62 8 70 0.00000 Bacillus sp. NSP9.1 1071078 S 1635 4 1639 0.00006 Bacillus sp. LJBS17 2859227 S 39 0 39 0.00000 Bacillus sp. ZY-1-1 2093834 S 12 6 18 0.00000 Bacillus sp. COPE52 2233998 S 12 4 16 0.00000 Bacillus sp. OxB-1 98228 S 11 0 11 0.00000 Bacillus sp. 7D3 2851015 S 10 0 10 0.00000 Bacillus thuringiensis 1428 S 255 177 432 0.00002 Bacillus cereus 1396 S 235 464 699 0.00003 Bacillus anthracis 1392 S 166 254 420 0.00002 Bacillus mycoides 1405 S 86 1 87 0.00000 Bacillus wiedmannii 1890302 S 65 0 65 0.00000 Bacillus cytotoxicus 580165 S 13 0 13 0.00000 Bacillus pseudomycoides 64104 S 12 0 12 0.00000 Bacillus altitudinis 293387 S 32 1 33 0.00000 Bacillus aquiflavi 2672567 S 21 0 21 0.00000 Bacillus safensis 561879 S 11 0 11 0.00000 Bacillus methanolicus 1471 S 10 0 10 0.00000 Anoxybacillus sediminis 2613334 S 5062 0 5062 0.00019 Lysinibacillus sphaericus 1421 S 59 20 79 0.00000 Lysinibacillus timonensis 2086577 S 31 0 31 0.00000 Lysinibacillus sp. SGAir0095 2070463 S 14 0 14 0.00000 Lysinibacillus agricola 2590012 S 11 0 11 0.00000 Metabacillus sp. B2-18 2897333 S 85 0 85 0.00000 Metabacillus endolithicus 1535204 S 24 0 24 0.00000 Metabacillus litoralis 152268 S 11 3 14 0.00000 Priestia megaterium 1404 S 28 14 42 0.00000 Priestia flexa 86664 S 19 0 19 0.00000 Virgibacillus sp. 6R 1911587 S 21 6 27 0.00000 Virgibacillus sp. Bac330 2419841 S 11 0 11 0.00000 Cytobacillus oceanisediminis 665099 S 38 0 38 0.00000 Weizmannia coagulans 1398 S 28 4 32 0.00000 Niallia circulans 1397 S 22 0 22 0.00000 Gracilibacillus sp. SSPM10-3 2932255 S 15 0 15 0.00000 Heyndrickxia oleronia 38875 S 12 0 12 0.00000 Halalkalibacterium halodurans 86665 S 14 3 17 0.00000 Neobacillus mesonae 1193713 S 10 0 10 0.00000 Anaerobacillus isosaccharinicus 1532552 S 11 0 11 0.00000 Listeria monocytogenes 1639 S 3960 262 4222 0.00016 Listeria innocua 1642 S 61 12 73 0.00000 Listeria grayi 1641 S 28 0 28 0.00000 Listeria ivanovii 1638 S 11 0 11 0.00000 Brochothrix thermosphacta 2756 S 1155 17 1172 0.00004 Brevibacillus laterosporus 1465 S 287 67 354 0.00001 Paenibacillus physcomitrellae 1619311 S 31 19 50 0.00000 Paenibacillus larvae 1464 S 24 81 105 0.00000 Paenibacillus bovis 1616788 S 22 2 24 0.00000 Paenibacillus sonchi 373687 S 20 17 37 0.00000 Paenibacillus jilunlii 682956 S 17 21 38 0.00000 Paenibacillus uliginis 683737 S 11 1 12 0.00000 Sporosarcina sp. PTS2304 2283194 S 64 5 69 0.00000 Solibacillus silvestris 76853 S 38 2 40 0.00000 Solibacillus sp. R5-41 2048654 S 17 0 17 0.00000 Planococcus sp. 107-1 2908840 S 14 0 14 0.00000 Planococcus antarcticus 161360 S 11 7 18 0.00000 Exiguobacterium sp. S3-2 1389960 S 20 24 44 0.00000 Thermoactinomyces vulgaris 2026 S 41 0 41 0.00000 [Ruminococcus] gnavus 33038 S 351 64 415 0.00002 [Ruminococcus] torques 33039 S 22 5 27 0.00000 Blautia obeum 40520 S 86 13 99 0.00000 Blautia sp. SC05B48 2479767 S 42 5 47 0.00000 Blautia sp. NBRC 113351 2877527 S 19 0 19 0.00000 Blautia producta 33035 S 55 1 56 0.00000 Blautia massiliensis 1737424 S 40 0 40 0.00000 Blautia argi 1912897 S 31 1 32 0.00000 Blautia hansenii 1322 S 24 8 32 0.00000 Blautia pseudococcoides 1796616 S 20 554 574 0.00002 Anaerostipes hadrus 649756 S 333 27 360 0.00001 Anaerobutyricum hallii 39488 S 149 40 189 0.00001 Coprococcus comes 410072 S 102 20 122 0.00000 Coprococcus catus 116085 S 27 3 30 0.00000 Enterocloster bolteae 208479 S 88 8 96 0.00000 Enterocloster clostridioformis 1531 S 25 55 80 0.00000 Sellimonas intestinalis 1653434 S 83 0 83 0.00000 [Clostridium] scindens 29347 S 56 3 59 0.00000 Faecalicatena sp. Marseille-Q4148 2823316 S 50 0 50 0.00000 Roseburia intestinalis 166486 S 21 6 27 0.00000 Roseburia hominis 301301 S 14 3 17 0.00000 Dorea longicatena 88431 S 31 0 31 0.00000 Anaerocolumna cellulosilytica 433286 S 12 0 12 0.00000 Lachnospira eligens 39485 S 14 0 14 0.00000 Ruthenibacterium lactatiformans 1550024 S 1403 14 1417 0.00005 Pseudoclostridium thermosuccinogenes 84032 S 34 0 34 0.00000 Caproiciproducens sp. NJN-50 2507162 S 33 0 33 0.00000 Faecalibacterium prausnitzii 853 S 25 0 25 0.00000 Solibaculum mannosilyticum 2780922 S 20 0 20 0.00000 Flavonifractor plautii 292800 S 20 0 20 0.00000 Clostridioides difficile 1496 S 1266 173 1439 0.00005 Clostridium perfringens 1502 S 77 1 78 0.00000 Clostridium tetani 1513 S 35 0 35 0.00000 Clostridium botulinum 1491 S 12 15 27 0.00000 Clostridium intestinale 36845 S 12 0 12 0.00000 Clostridium tyrobutyricum 1519 S 11 0 11 0.00000 Clostridium beijerinckii 1520 S 11 2 13 0.00000 Eubacterium sp. NSJ-61 2764325 S 56 2 58 0.00000 Mogibacterium pumilum 86332 S 25 2 27 0.00000 Christensenella minuta 626937 S 20 0 20 0.00000 Veillonella parvula 29466 S 857 2 859 0.00003 Phascolarctobacterium faecium 33025 S 21 1 22 0.00000 Parvimonas micra 33033 S 625 22 647 0.00002 Amedibacterium intestinale 2583452 S 145 6 151 0.00001 [Clostridium] innocuum 1522 S 73 1 74 0.00000 Erysipelatoclostridium ramosum 1547 S 68 0 68 0.00000 Faecalibacillus intestinalis 1982626 S 98 17 115 0.00000 Erysipelothrix larvae 1514105 S 17 0 17 0.00000 Erysipelothrix rhusiopathiae 1648 S 14 0 14 0.00000 Longicatena caecimuris 1796635 S 25 0 25 0.00000 Turicibacter sp. TJ11 2806443 S 10 0 10 0.00000 Actinomyces sp. oral taxon 414 712122 S 136 13 149 0.00001 Arcanobacterium haemolyticum 28264 S 21 2 23 0.00000 Schaalia odontolytica 1660 S 10 0 10 0.00000 Mycobacterium tuberculosis 1773 S 17 8 25 0.00000 Bifidobacterium longum 216816 S 53 3 56 0.00000 Cutibacterium acnes 1747 S 14 1 15 0.00000 Eggerthella lenta 84112 S 135 12 147 0.00001 Mycoplasma mycoides 2102 S 250 2 252 0.00001 Mycoplasma capricolum 2095 S 24 6 30 0.00000 Mycoplasmopsis bovirhinis 29553 S 32 0 32 0.00000 Mycoplasmopsis gallinacea 29556 S 19 0 19 0.00000 Klebsiella pneumoniae 573 S 460831 1030977 1491808 0.05550 Klebsiella quasipneumoniae 1463165 S 4116 19763 23879 0.00089 Klebsiella variicola 244366 S 4115 7438 11553 0.00043 Klebsiella quasivariicola 2026240 S 1304 483 1787 0.00007 Klebsiella africana 2489010 S 959 238 1197 0.00004 Klebsiella sp. WP4-W18-ESBL-05 2675713 S 547 1351 1898 0.00007 Klebsiella sp. PL-2018 2851540 S 46 0 46 0.00000 Klebsiella sp. CTHL.F3a 2873296 S 45 0 45 0.00000 Klebsiella sp. A52 2834819 S 43 0 43 0.00000 Klebsiella sp. KPN54798 2897413 S 30 0 30 0.00000 Klebsiella sp. P1CD1 2267618 S 21 129 150 0.00001 Klebsiella aerogenes 548 S 815 92 907 0.00003 Klebsiella michiganensis 1134687 S 547 11082 11629 0.00043 Klebsiella oxytoca 571 S 519 180 699 0.00003 Klebsiella grimontii 2058152 S 241 1042 1283 0.00005 Klebsiella huaxiensis 2153354 S 124 13 137 0.00001 Raoultella ornithinolytica 54291 S 316 170 486 0.00002 Raoultella planticola 575 S 56 5 61 0.00000 Raoultella sp. XY-1 2799495 S 10 38 48 0.00000 Escherichia coli 562 S 2179 23338 25517 0.00095 Escherichia fergusonii 564 S 17 4 21 0.00000 Escherichia marmotae 1499973 S 17 1 18 0.00000 Escherichia albertii 208962 S 13 1 14 0.00000 Enterobacter cloacae complex sp. ECL411 2912629 S 232 0 232 0.00001 Enterobacter cloacae complex sp. 2027919 S 51 23 74 0.00000 Enterobacter hormaechei 158836 S 267 223 490 0.00002 Enterobacter cloacae 550 S 224 59 283 0.00001 Enterobacter roggenkampii 1812935 S 201 75 276 0.00001 Enterobacter asburiae 61645 S 38 12 50 0.00000 Enterobacter kobei 208224 S 25 14 39 0.00000 Enterobacter ludwigii 299767 S 11 2 13 0.00000 Enterobacter cancerogenus 69218 S 10 0 10 0.00000 Enterobacter sp. JBIWA005 2831891 S 609 0 609 0.00002 Enterobacter sp. DNB-S2 2720029 S 14 0 14 0.00000 Enterobacter mori 539813 S 277 81 358 0.00001 Salmonella enterica 28901 S 368 1315 1683 0.00006 Salmonella sp. 599 S 43 1737 1780 0.00007 Citrobacter freundii 546 S 137 88 225 0.00001 Citrobacter portucalensis 1639133 S 33 40 73 0.00000 Citrobacter arsenatis 2546350 S 66 9 75 0.00000 Citrobacter amalonaticus 35703 S 14 10 24 0.00000 Leclercia adecarboxylata 83655 S 176 35 211 0.00001 Leclercia sp. J807 2681307 S 62 2 64 0.00000 Shigella boydii 621 S 84 252 336 0.00001 Shigella flexneri 623 S 64 214 278 0.00001 Shigella dysenteriae 622 S 12 136 148 0.00001 Cronobacter sakazakii 28141 S 35 47 82 0.00000 Cronobacter universalis 535744 S 13 0 13 0.00000 Kosakonia radicincitans 283686 S 16 19 35 0.00000 Yokenella regensburgei 158877 S 38 1 39 0.00000 Jejubacter calystegiae 2579935 S 29 0 29 0.00000 Pluralibacter gergoviae 61647 S 10 0 10 0.00000 Lelliottia amnigena 61646 S 14 0 14 0.00000 Pectobacterium aquaticum 2204145 S 1547 0 1547 0.00006 Serratia fonticola 47917 S 723 13 736 0.00003 Serratia marcescens 615 S 42 6 48 0.00000 Serratia symbiotica 138074 S 11 0 11 0.00000 Yersinia ruckeri 29486 S 246 3 249 0.00001 Pantoea stewartii 66269 S 333 15 348 0.00001 Pantoea agglomerans 549 S 14 0 14 0.00000 Pantoea dispersa 59814 S 11 0 11 0.00000 Proteus mirabilis 584 S 19 2 21 0.00000 Arsenophonus endosymbiont of Aphis craccivora 1231049 S 14 0 14 0.00000 Morganella morganii 582 S 11 8 19 0.00000 Edwardsiella tarda 636 S 10 5 15 0.00000 Vibrio cholerae 666 S 13 1 14 0.00000 Photobacterium damselae 38293 S 11 1 12 0.00000 Gallibacterium anatis 750 S 12 0 12 0.00000 Acinetobacter baumannii 470 S 17 6 23 0.00000 Campylobacter coli 195 S 398 5 403 0.00001 Campylobacter jejuni 197 S 58 5 63 0.00000 Campylobacter sp. RM10537 1032242 S 10 0 10 0.00000 Helicobacter pylori 210 S 12 0 12 0.00000 Neisseria meningitidis 487 S 12 3 15 0.00000 Prevotella nigrescens 28133 S 48 0 48 0.00000 Prevotella enoeca 76123 S 42 11 53 0.00000 Prevotella intermedia 28131 S 11 4 15 0.00000 Phocaeicola vulgatus 821 S 34 22 56 0.00000 Tannerella forsythia 28112 S 14 1 15 0.00000 Porphyromonas endodontalis 28124 S 20 0 20 0.00000 Butyricimonas faecalis 2093856 S 12 11 23 0.00000 Polaribacter sp. HaHaR_3_91 2745561 S 13 0 13 0.00000 Treponema sp. Marseille-Q4132 2766701 S 15 2 17 0.00000 Treponema socranskii 53419 S 15 2 17 0.00000 Fusobacterium necrophorum 859 S 24 1 25 0.00000 Fusobacterium nucleatum 851 S 18 0 18 0.00000 Homo sapiens 9606 S 363 0 363 0.00001 Malassezia restricta 76775 S 20 0 20 0.00000 Sporisorium graminicola 280036 S 10 0 10 0.00000