Mercurial > repos > youyuh48 > combine_bracken_outputs
comparison test-data/sample2_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 |
| parents | |
| children |
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| -1:000000000000 | 0:6e90a30b214f |
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| 1 name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads | |
| 2 Streptococcus sanguinis 1305 S 21 0 21 0.00000 | |
| 3 Streptococcus suis 1307 S 22 1 23 0.00000 | |
| 4 Streptococcus gordonii 1302 S 10 0 10 0.00000 | |
| 5 Vibrio cholerae 666 S 10 4 14 0.00000 | |
| 6 Bacillus methylotrophicus 492670 S 23 0 23 0.00000 | |
| 7 Streptococcus thermophilus 1308 S 34 0 34 0.00000 | |
| 8 Streptococcus mutans 1309 S 10 0 10 0.00000 | |
| 9 Burkholderia xenovorans 36873 S 34 0 34 0.00000 | |
| 10 Sinorhizobium medicae 110321 S 54 0 54 0.00000 | |
| 11 Burkholderia phymatum 148447 S 655478 1228 656706 0.02503 | |
| 12 Borrelia burgdorferi 139 S 36 0 36 0.00000 | |
| 13 Nostoc punctiforme 272131 S 590086 562 590648 0.02251 | |
| 14 Shewanella frigidimarina 56812 S 23 0 23 0.00000 | |
| 15 Clostridium novyi 1542 S 211808 388 212196 0.00809 | |
| 16 Mycobacterium tuberculosis 1773 S 20647 274350 294997 0.01124 | |
| 17 Mycobacterium smegmatis 1772 S 239 0 239 0.00001 | |
| 18 Rhodopseudomonas palustris 1076 S 823190 1106 824296 0.03141 | |
| 19 Bacteroides thetaiotaomicron 818 S 392179 3490 395669 0.01508 | |
| 20 Mycobacterium abscessus 36809 S 78 0 78 0.00000 | |
| 21 Burkholderia multivorans 87883 S 30 5 35 0.00000 | |
| 22 Citrobacter koseri 545 S 576 17 593 0.00002 | |
| 23 Bordetella pertussis 520 S 632 732 1364 0.00005 | |
| 24 Chlamydia trachomatis 813 S 71933 284 72217 0.00275 | |
| 25 Pseudomonas aeruginosa 287 S 42 1 43 0.00000 | |
| 26 Chlamydia pneumoniae 83558 S 78615 83 78698 0.00300 | |
| 27 Haloquadratum walsbyi 293091 S 223986 31 224017 0.00854 | |
| 28 Streptococcus pyogenes 1314 S 252007 4976 256983 0.00979 | |
| 29 Streptococcus pneumoniae 1313 S 177347 1168 178515 0.00680 | |
| 30 Pelodictyon luteolum 1100 S 157283 1662 158945 0.00606 | |
| 31 Streptococcus agalactiae 1311 S 159789 4251 164040 0.00625 | |
| 32 Pseudomonas protegens 380021 S 18 0 18 0.00000 | |
| 33 Salmonella enterica 28901 S 387186 4916 392102 0.01494 | |
| 34 Francisella tularensis 263 S 120338 554 120892 0.00461 | |
| 35 Clostridium botulinum 1491 S 281791 594 282385 0.01076 | |
| 36 Alkaliphilus metalliredigens 208226 S 368065 432 368497 0.01404 | |
| 37 Shewanella denitrificans 192073 S 17 0 17 0.00000 | |
| 38 Shewanella sp. MR-7 60481 S 224465 86579 311044 0.01185 | |
| 39 Bacillus licheniformis 1402 S 13 0 13 0.00000 | |
| 40 Burkholderia ambifaria 152480 S 27 3 30 0.00000 | |
| 41 Alkalilimnicola ehrlichii 351052 S 226337 74 226411 0.00863 | |
| 42 Corynebacterium jeikeium 38289 S 20 0 20 0.00000 | |
| 43 Pediococcus pentosaceus 1255 S 13 0 13 0.00000 | |
| 44 Bacillus anthracis 1392 S 151306 277437 428743 0.01634 | |
| 45 Hyphomonas neptunium 81032 S 262956 33 262989 0.01002 | |
| 46 Borrelia afzelii 29518 S 37 0 37 0.00000 | |
| 47 Pseudomonas fluorescens 294 S 21 1 22 0.00000 | |
| 48 Corynebacterium urealyticum 43771 S 168078 3426 171504 0.00654 | |
| 49 Bacillus clausii 79880 S 281618 346 281964 0.01075 | |
| 50 Campylobacter concisus 199 S 157661 329 157990 0.00602 | |
| 51 Shewanella baltica 62322 S 108 1 109 0.00000 | |
| 52 Pseudomonas stutzeri 316 S 293151 1980 295131 0.01125 | |
| 53 Cytophaga hutchinsonii 985 S 307508 31 307539 0.01172 | |
| 54 Cyanothece sp. ATCC 51142 43989 S 372257 54 372311 0.01419 | |
| 55 Thermus thermophilus 274 S 152701 13 152714 0.00582 | |
| 56 Bacillus cytotoxicus 580165 S 643 5 648 0.00002 | |
| 57 Clostridium acetobutylicum 1488 S 13 0 13 0.00000 | |
| 58 Burkholderia cenocepacia 95486 S 29 50 79 0.00000 | |
| 59 Corynebacterium efficiens 152794 S 233423 670 234093 0.00892 | |
| 60 Chromobacterium violaceum 536 S 330985 434 331419 0.01263 | |
| 61 Ureaplasma parvum 134821 S 47612 5 47617 0.00181 | |
| 62 Bacillus pumilus 1408 S 20 0 20 0.00000 | |
| 63 Enterobacter sp. 638 399742 S 290 1 291 0.00001 | |
| 64 Bordetella avium 521 S 81 0 81 0.00000 | |
| 65 Bacillus cereus 1396 S 1086754 202070 1288824 0.04912 | |
| 66 Ochrobactrum anthropi 529 S 381841 1054 382895 0.01459 | |
| 67 Thermosipho melanesiensis 46541 S 128132 53 128185 0.00489 | |
| 68 Mycobacterium marinum 1781 S 281340 152004 433344 0.01651 | |
| 69 Nostoc sp. PCC 7120 103690 S 247 7 254 0.00001 | |
| 70 Pseudomonas mendocina 300 S 14 1 15 0.00000 | |
| 71 Lactococcus lactis 1358 S 404921 2772 407693 0.01554 | |
| 72 Pseudomonas putida 303 S 511201 4777 515978 0.01966 | |
| 73 Sinorhizobium meliloti 382 S 420783 3928 424711 0.01619 | |
| 74 Clostridium beijerinckii 1520 S 418932 1011 419943 0.01600 | |
| 75 Geobacillus thermodenitrificans 33940 S 11 11 22 0.00000 | |
| 76 Saccharopolyspora erythraea 1836 S 10 0 10 0.00000 | |
| 77 Shewanella oneidensis 70863 S 222 4 226 0.00001 | |
| 78 Bradyrhizobium sp. ORS 278 114615 S 14 5 19 0.00000 | |
| 79 Rickettsia typhi 785 S 43 0 43 0.00000 | |
| 80 Methanococcus maripaludis 39152 S 121232 302 121534 0.00463 | |
| 81 Rickettsia prowazekii 782 S 70541 1619 72160 0.00275 | |
| 82 Listeria innocua 1642 S 33 1 34 0.00000 | |
| 83 Bordetella petrii 94624 S 233 5 238 0.00001 | |
| 84 Bradyrhizobium diazoefficiens 1355477 S 17 0 17 0.00000 | |
| 85 Mycobacterium sp. KMS 189918 S 11 267 278 0.00001 | |
| 86 Bordetella parapertussis 519 S 348 1146 1494 0.00006 | |
| 87 Bordetella bronchiseptica 518 S 128479 327016 455495 0.01736 | |
| 88 Staphylococcus saprophyticus 29385 S 34 0 34 0.00000 | |
| 89 Listeria monocytogenes 1639 S 43 1 44 0.00000 | |
| 90 Cupriavidus taiwanensis 164546 S 12 0 12 0.00000 | |
| 91 Chlamydophila caviae 83557 S 74403 340 74743 0.00285 | |
| 92 Candidatus Blochmannia pennsylvanicus 101534 S 52480 50 52530 0.00200 | |
| 93 Shigella flexneri 623 S 1022 4135 5157 0.00020 | |
| 94 Shigella dysenteriae 622 S 1206 1447 2653 0.00010 | |
| 95 Shigella boydii 621 S 1035 3475 4510 0.00017 | |
| 96 Rhodococcus jostii 132919 S 622004 310 622314 0.02372 | |
| 97 Shigella sonnei 624 S 605 1923 2528 0.00010 | |
| 98 Klebsiella pneumoniae 573 S 333 5 338 0.00001 | |
| 99 Sodalis glossinidius 63612 S 292996 614 293610 0.01119 | |
| 100 Nitrosococcus oceani 1229 S 13 0 13 0.00000 | |
| 101 Shewanella sp. MR-4 60480 S 336 137 473 0.00002 | |
| 102 Neisseria meningitidis 487 S 143635 11544 155179 0.00591 | |
| 103 Herpetosiphon aurantiacus 65 S 427279 27 427306 0.01628 | |
| 104 Leptospira borgpetersenii 174 S 242592 345 242937 0.00926 | |
| 105 Leptospira interrogans 173 S 13 0 13 0.00000 | |
| 106 Photobacterium profundum 74109 S 12 1 13 0.00000 | |
| 107 Lysinibacillus sphaericus 1421 S 47 0 47 0.00000 | |
| 108 Clostridium perfringens 1502 S 17 0 17 0.00000 | |
| 109 Bacillus subtilis 1423 S 265462 2267 267729 0.01020 | |
| 110 Lawsonia intracellularis 29546 S 114759 23 114782 0.00437 | |
| 111 Lactobacillus casei 1582 S 11 0 11 0.00000 | |
| 112 Bacillus thuringiensis 1428 S 187882 159705 347587 0.01325 | |
| 113 Psychrobacter arcticus 334543 S 78 0 78 0.00000 | |
| 114 Oceanobacillus iheyensis 182710 S 15 0 15 0.00000 | |
| 115 Lactobacillus helveticus 1587 S 12 0 12 0.00000 | |
| 116 Lactobacillus delbrueckii 1584 S 153860 3163 157023 0.00598 | |
| 117 Histophilus somni 731 S 136275 317 136592 0.00521 | |
| 118 Wigglesworthia glossinidia 51229 S 66219 57 66276 0.00253 | |
| 119 Cronobacter sakazakii 28141 S 270 3 273 0.00001 | |
| 120 Yersinia enterocolitica 630 S 101 0 101 0.00000 | |
| 121 Bacillus halodurans 86665 S 269485 450 269935 0.01029 | |
| 122 Yersinia pestis 632 S 61383 252873 314256 0.01198 | |
| 123 Burkholderia vietnamiensis 60552 S 26 5 31 0.00000 | |
| 124 Photorhabdus luminescens 29488 S 51 0 51 0.00000 | |
| 125 Bacillus weihenstephanensis 86662 S 1934 51 1985 0.00008 | |
| 126 Idiomarina loihiensis 135577 S 187227 435 187662 0.00715 | |
| 127 Prochlorococcus marinus 1219 S 307019 266 307285 0.01171 | |
| 128 Ignicoccus hospitalis 160233 S 87443 14 87457 0.00333 | |
| 129 Burkholderia lata 482957 S 16 2 18 0.00000 | |
| 130 Lactobacillus salivarius 1624 S 139242 326 139568 0.00532 | |
| 131 Syntrophomonas wolfei 863 S 193716 30 193746 0.00738 | |
| 132 Burkholderia thailandensis 57975 S 1133 49 1182 0.00005 | |
| 133 Haemophilus influenzae 727 S 117883 629 118512 0.00452 | |
| 134 Cupriavidus necator 106590 S 29061 136 29197 0.00111 | |
| 135 Acinetobacter sp. ADP1 62977 S 11 0 11 0.00000 | |
| 136 Ruminiclostridium thermocellum 1515 S 260096 100 260196 0.00992 | |
| 137 Erwinia tasmaniensis 338565 S 322076 1182 323258 0.01232 | |
| 138 Clostridium tetani 1513 S 16 0 16 0.00000 | |
| 139 Psychrobacter cryohalolentis 330922 S 413504 4426 417930 0.01593 | |
| 140 Borrelia bavariensis 664662 S 78122 1938 80060 0.00305 | |
| 141 Shewanella loihica 359303 S 10 0 10 0.00000 | |
| 142 Pasteurella multocida 747 S 12 0 12 0.00000 | |
| 143 Treponema denticola 158 S 183744 23 183767 0.00700 | |
| 144 Yersinia pseudotuberculosis 633 S 709 1324 2033 0.00008 | |
| 145 Pseudomonas entomophila 312306 S 52 0 52 0.00000 | |
| 146 Halorhodospira halophila 1053 S 11 0 11 0.00000 | |
| 147 Lachnoclostridium phytofermentans 66219 S 10 0 10 0.00000 | |
| 148 Buchnera aphidicola 9 S 26192 14 26206 0.00100 | |
| 149 Escherichia coli 562 S 717629 732184 1449813 0.05525 | |
| 150 Coxiella burnetii 777 S 135506 22 135528 0.00516 | |
| 151 Geobacter sulfurreducens 35554 S 244079 217 244296 0.00931 | |
| 152 Anabaena variabilis 1172 S 433603 12868 446471 0.01701 | |
| 153 Synechococcus elongatus 32046 S 466278 215 466493 0.01778 | |
| 154 Serratia proteamaculans 28151 S 117 0 117 0.00000 | |
| 155 Burkholderia pseudomallei 28450 S 224374 228836 453210 0.01727 | |
| 156 Neisseria gonorrhoeae 485 S 135601 16923 152524 0.00581 | |
| 157 Thiobacillus denitrificans 36861 S 226889 122 227011 0.00865 | |
| 158 Burkholderia mallei 13373 S 193 3075 3268 0.00012 | |
| 159 Pectobacterium atrosepticum 29471 S 96 0 96 0.00000 | |
| 160 Listeria welshimeri 1643 S 176044 4791 180835 0.00689 | |
| 161 Mycobacterium gilvum 1804 S 236 8 244 0.00001 | |
| 162 Mycobacterium sp. JLS 164757 S 326114 373821 699935 0.02667 | |
| 163 Staphylococcus aureus 1280 S 1192940 19301 1212241 0.04620 | |
| 164 Staphylococcus haemolyticus 1283 S 33 0 33 0.00000 | |
| 165 Staphylococcus epidermidis 1282 S 53 2 55 0.00000 | |
| 166 Psychromonas ingrahamii 357794 S 287498 273 287771 0.01097 | |
| 167 Shewanella amazonensis 60478 S 18 0 18 0.00000 | |
| 168 Mycobacterium vanbaalenii 110539 S 244 4 248 0.00001 | |
| 169 Shewanella sediminis 271097 S 12 0 12 0.00000 | |
| 170 Acinetobacter baumannii 470 S 257301 727 258028 0.00983 | |
| 171 Mycobacterium leprae 1769 S 31 0 31 0.00000 | |
| 172 Mycobacterium bovis 1765 S 15035 264359 279394 0.01065 | |
| 173 Mycobacterium ulcerans 1809 S 525 376 901 0.00003 | |
| 174 Vibrio campbellii 680 S 11 3 14 0.00000 | |
| 175 Mycobacterium avium 1764 S 310855 356 311211 0.01186 | |
| 176 Shewanella sp. ANA-3 94122 S 405 42 447 0.00002 |