Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads
diff test-data/input/README.md @ 0:3ab9d37e547e draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 0d1d1f356cdfd8ef6dbcdd1bfe76c4637587ff53"
| author | public-health-bioinformatics |
|---|---|
| date | Thu, 10 Mar 2022 21:35:14 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/README.md Thu Mar 10 21:35:14 2022 +0000 @@ -0,0 +1,32 @@ + + +## Obtain original sequence data + +``` +wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/049/SRR17619849/SRR17619849_1.fastq.gz +wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/049/SRR17619849/SRR17619849_2.fastq.gz +wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR179/045/SRR17907745/SRR17907745_1.fastq.gz +wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR179/045/SRR17907745/SRR17907745_2.fastq.gz +``` + +## Obtain kraken2/bracken database + +large file ~38GB compressed, ~50GB uncompressed + +``` +wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20210517.tar.gz +``` + +## Run kraken2 + +``` +kraken2 --db k2_standard_20210517 --report --report SRR17619849_kraken2.txt --paired SRR17619849_1.fastq.gz SRR17619849_2.fastq.gz +kraken2 --db k2_standard_20210517 --report --report SRR17907745_kraken2.txt --paired SRR17907745_1.fastq.gz SRR17907745_2.fastq.gz +``` + +## Run bracken + +``` +bracken -d k2_standard_20210517 -i SRR17619849_kraken2.txt -o SRR17619849_bracken_abundances.tsv -r 250 -l S +bracken -d k2_standard_20210517 -i SRR17907745_kraken2.txt -o SRR17907745_bracken_abundances.tsv -r 150 -l S +```