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Add Kraken 1 and KrakenUniq report tests
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@fbreitwieser
fbreitwieser committed Apr 13, 2021
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6 changes: 5 additions & 1 deletion README.md
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Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as
Kraken, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.

For more information look at the preprint at http://biorxiv.org/content/early/2016/10/31/084715.full.pdf+html . Please cite the preprint if you use Pavian in your research.
For more information look at the publication at https://doi.org/10.1093/bioinformatics/btz715

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. FP Breitwieser, SL Salzberg - Bioinformatics, 2020

Thank you for citing the publication if Pavian helps in your research :).

You can try out Pavian at https://fbreitwieser.shinyapps.io/pavian/.

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6,064 changes: 0 additions & 6,064 deletions tests/testthat/read_report/input/k2uniq-report.txt
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100 changes: 100 additions & 0 deletions tests/testthat/read_report/input/kraken-report.txt
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0.62 212758 212758 U 0 unclassified
99.38 34120071 149908 - 1 root
98.51 33819699 134 - 131567 cellular organisms
98.45 33801051 4375 D 2 Bacteria
44.58 15304881 16363 P 1224 Proteobacteria
25.80 8858966 8538 C 1236 Gammaproteobacteria
9.62 3304270 21338 O 91347 Enterobacterales
6.39 2194601 135397 F 543 Enterobacteriaceae
2.70 927482 48597 G 570 Klebsiella
1.93 660954 659371 S 571 Klebsiella oxytoca
0.00 399 0 - 1000005996 GCF_001548355.1 Klebsiella oxytoca strain=JKo3
0.00 393 393 - 1000005997 NZ_AP014951.1 Klebsiella oxytoca DNA, complete genome, strain: JKo3
0.00 5 5 - 1000005998 NZ_AP014952.1 Klebsiella oxytoca plasmid pKO_JKo3_1 DNA, complete genome, strain: JKo3
0.00 1 1 - 1000006001 NZ_AP014955.1 Klebsiella oxytoca plasmid pKO_JKo3_4 DNA, complete genome, strain: JKo3
0.00 398 0 - 1000005989 GCF_001022295.1 Klebsiella oxytoca strain=CAV1099
0.00 317 317 - 1000005990 NZ_CP011597.1 Klebsiella oxytoca strain CAV1099, complete genome
0.00 81 81 - 1000005994 NZ_CP011593.1 Klebsiella oxytoca strain CAV1099 plasmid pCAV1099-69, complete sequence
0.00 326 0 - 1000005976 GCF_001022195.1 Klebsiella oxytoca strain=CAV1374
0.00 324 324 - 1000005977 NZ_CP011636.1 Klebsiella oxytoca strain CAV1374, complete genome
0.00 1 1 - 1000005979 NZ_CP011633.1 Klebsiella oxytoca strain CAV1374 plasmid pCAV1374-150, complete sequence
0.00 1 1 - 1000005980 NZ_CP011628.1 Klebsiella oxytoca strain CAV1374 plasmid pCAV1374-16, complete sequence
0.00 293 0 - 1000006016 GCF_002072655.1 Klebsiella oxytoca strain=AR_0147
0.00 292 292 - 1000006017 NZ_CP020358.1 Klebsiella oxytoca strain AR_0147, complete genome
0.00 1 1 - 1000006018 NZ_CP020359.1 Klebsiella oxytoca strain AR_0147 plasmid unitig_2, complete sequence
0.00 110 0 - 1333852 Klebsiella oxytoca KONIH1
0.00 110 0 - 1000005964 GCF_000714655.1 Klebsiella oxytoca KONIH1
0.00 110 110 - 1000005965 NZ_CP008788.1 Klebsiella oxytoca KONIH1, complete genome
0.00 40 0 - 1000006002 GCF_001970835.1 Klebsiella oxytoca strain=CAV1752
0.00 26 26 - 1000006005 NZ_CP018361.1 Klebsiella oxytoca strain CAV1752 plasmid pCAV1752-278, complete sequence
0.00 13 13 - 1000006003 NZ_CP018362.1 Klebsiella oxytoca strain CAV1752, complete genome
0.00 1 1 - 1000006004 NZ_CP018360.1 Klebsiella oxytoca strain CAV1752 plasmid pCAV1752-111, complete sequence
0.00 15 0 - 1000005969 GCF_001022115.1 Klebsiella oxytoca strain=CAV1335
0.00 15 15 - 1000005970 NZ_CP011618.1 Klebsiella oxytoca strain CAV1335, complete genome
0.00 2 0 - 1000006009 GCF_001870185.1 Klebsiella oxytoca strain=CAV1015
0.00 2 2 - 1000006010 NZ_CP017928.1 Klebsiella oxytoca strain CAV1015 chromosome, complete genome
0.60 206219 0 S 2026240 Klebsiella quasivariicola
0.60 206219 156 - 1000024047 GCF_002269255.1 Klebsiella quasivariicola strain=KPN1705
0.59 203947 203947 - 1000024048 NZ_CP022823.1 Klebsiella quasivariicola strain KPN1705 chromosome, complete genome
0.00 1333 1333 - 1000024049 NZ_CP022824.1 Klebsiella quasivariicola strain KPN1705 plasmid pKPN1705-1, complete sequence
0.00 727 727 - 1000024050 NZ_CP022825.1 Klebsiella quasivariicola strain KPN1705 plasmid pKPN1705-2, complete sequence
0.00 56 56 - 1000024051 NZ_CP022826.1 Klebsiella quasivariicola strain KPN1705 plasmid pKPN1705-3, complete sequence
0.03 10987 10033 S 573 Klebsiella pneumoniae
0.00 333 29 - 72407 Klebsiella pneumoniae subsp. pneumoniae
0.00 142 0 - 1193292 Klebsiella pneumoniae subsp. pneumoniae 1084
0.00 142 0 - 1000006054 GCF_000294365.1 Klebsiella pneumoniae subsp. pneumoniae 1084
0.00 142 142 - 1000006055 NC_018522.1 Klebsiella pneumoniae subsp. pneumoniae 1084, complete genome
0.00 33 0 - 1000006252 GCF_001529935.1 Klebsiella pneumoniae subsp. pneumoniae strain=RJF999
0.00 32 32 - 1000006254 NZ_CP014011.1 Klebsiella pneumoniae subsp. pneumoniae strain RJF999 plasmid pRJF999, complete sequence
0.00 1 1 - 1000006253 NZ_CP014010.1 Klebsiella pneumoniae subsp. pneumoniae strain RJF999, complete genome
0.00 29 0 - 1123862 Klebsiella pneumoniae subsp. pneumoniae Kp13
0.00 29 0 - 1000006091 GCF_000512165.1 Klebsiella pneumoniae subsp. pneumoniae Kp13
0.00 25 25 - 1000006092 NZ_CP003999.1 Klebsiella pneumoniae subsp. pneumoniae Kp13 chromosome, complete genome
0.00 3 3 - 1000006096 NZ_CP003997.1 Klebsiella pneumoniae subsp. pneumoniae Kp13 plasmid pKP13d, complete sequence
0.00 1 1 - 1000006095 NZ_CP003995.1 Klebsiella pneumoniae subsp. pneumoniae Kp13 plasmid pKP13c, complete sequence
0.00 17 0 - 1125630 Klebsiella pneumoniae subsp. pneumoniae HS11286
0.00 17 0 - 1000006036 GCF_000240185.1 Klebsiella pneumoniae subsp. pneumoniae HS11286
0.00 15 15 - 1000006037 NC_016845.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 chromosome, complete genome
0.00 1 1 - 1000006039 NC_016846.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS2, complete sequence
0.00 1 1 - 1000006042 NC_016847.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 plasmid pKPHS5, complete sequence
0.00 11 0 - 1000006159 GCF_000784945.1 Klebsiella pneumoniae subsp. pneumoniae strain=KPNIH29
0.00 9 9 - 1000006160 NZ_CP009863.1 Klebsiella pneumoniae subsp. pneumoniae strain KPNIH29, complete genome
0.00 2 2 - 1000006162 NZ_CP009865.1 Klebsiella pneumoniae subsp. pneumoniae strain KPNIH29 plasmid pKPN-80a, complete sequence
0.00 9 0 - 1000006197 GCF_000981845.1 Klebsiella pneumoniae subsp. pneumoniae strain=234-12
0.00 8 8 - 1000006198 NZ_CP011313.1 Klebsiella pneumoniae subsp. pneumoniae strain 234-12, complete genome
0.00 1 1 - 1000006200 NZ_CP011314.1 Klebsiella pneumoniae subsp. pneumoniae strain 234-12 plasmid pKpn23412-362, complete sequence
0.00 9 0 - 1000006255 GCF_001530015.1 Klebsiella pneumoniae subsp. pneumoniae strain=RJF293
0.00 9 9 - 1000006256 NZ_CP014008.1 Klebsiella pneumoniae subsp. pneumoniae strain RJF293, complete genome
0.00 9 0 - 1392499 Klebsiella pneumoniae subsp. pneumoniae 1158
0.00 9 0 - 1000006186 GCF_000814805.1 Klebsiella pneumoniae subsp. pneumoniae 1158
0.00 9 9 - 1000006187 NZ_CP006722.1 Klebsiella pneumoniae subsp. pneumoniae 1158, complete genome
0.00 7 0 - 1000006266 GCF_001611055.1 Klebsiella pneumoniae subsp. pneumoniae strain=TGH8
0.00 7 7 - 1000006267 NZ_CP012743.1 Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome
0.00 7 0 - 1328324 Klebsiella pneumoniae subsp. pneumoniae KPNIH27
0.00 7 0 - 1000006118 GCF_000695935.1 Klebsiella pneumoniae subsp. pneumoniae KPNIH27
0.00 5 5 - 1000006119 NZ_CP007731.1 Klebsiella pneumoniae subsp. pneumoniae KPNIH27, complete genome
0.00 1 1 - 1000006122 NZ_CP007734.1 Klebsiella pneumoniae subsp. pneumoniae KPNIH27 plasmid pKPN-262, complete sequence
0.00 1 1 - 1000006123 NZ_CP007735.1 Klebsiella pneumoniae subsp. pneumoniae KPNIH27 plasmid pKPN-a41, complete sequence
0.00 6 0 - 1000006248 GCF_001521895.1 Klebsiella pneumoniae subsp. pneumoniae strain=NUHL24835
0.00 3 3 - 1000006249 NZ_CP014004.1 Klebsiella pneumoniae subsp. pneumoniae strain NUHL24835, complete genome
0.00 3 3 - 1000006250 NZ_CP014005.1 Klebsiella pneumoniae subsp. pneumoniae strain NUHL24835 plasmid unnamed1, complete sequence
0.00 5 0 - 1000006355 GCF_001746535.1 Klebsiella pneumoniae subsp. pneumoniae strain=TGH13
0.00 5 5 - 1000006356 NZ_CP012745.1 Klebsiella pneumoniae subsp. pneumoniae strain TGH13, complete genome
0.00 4 0 - 272620 Klebsiella pneumoniae subsp. pneumoniae MGH 78578
0.00 4 0 - 1000006022 GCF_000016305.1 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 strain=ATCC 700721; MGH 78578
0.00 3 3 - 1000006026 NC_009651.1 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN5, complete sequence
0.00 1 1 - 1000006023 NC_009648.1 Klebsiella pneumoniae subsp. pneumoniae MGH 78578, complete genome
0.00 4 0 - 1000006139 GCF_000742755.1 Klebsiella pneumoniae subsp. pneumoniae strain=ATCC 43816 KPPR1
0.00 4 4 - 1000006140 NZ_CP009208.1 Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
0.00 4 0 - 1000006264 GCF_001611095.1 Klebsiella pneumoniae subsp. pneumoniae strain=TGH10
0.00 4 4 - 1000006265 NZ_CP012744.1 Klebsiella pneumoniae subsp. pneumoniae strain TGH10, complete genome
0.00 3 0 - 1094170 Klebsiella pneumoniae subsp. pneumoniae KPNIH10
0.00 3 0 - 1000006044 GCF_000281435.2 Klebsiella pneumoniae subsp. pneumoniae KPNIH10
0.00 3 3 - 1000006045 NZ_CP007727.1 Klebsiella pneumoniae subsp. pneumoniae KPNIH10, complete genome
0.00 3 0 - 1000006595 GCF_002163895.1 Klebsiella pneumoniae subsp. pneumoniae strain=RJA166
0.00 3 3 - 1000006596 NZ_CP019047.1 Klebsiella pneumoniae subsp. pneumoniae strain RJA166 chromosome, complete genome
0.00 1 0 - 484021 Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
0.00 1 0 - 1000006019 GCF_000009885.1 Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
0.00 1 1 - 1000006020 NC_012731.1 Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 DNA, complete genome
0.00 1 0 - 1000006714 GCF_002249975.1 Klebsiella pneumoniae subsp. pneumoniae strain=AUSMDU00008079
0.00 1 1 - 1000006718 NZ_CP022694.1 Klebsiella pneumoniae subsp. pneumoniae strain AUSMDU00008079 plasmid pAUSMDU8079-3, complete sequence
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