Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads
view test-data/input/README.md @ 2:87459bd1615a draft
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 4ebe8216c423e2d66be92247f273df21cb5852f1
author | public-health-bioinformatics |
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date | Thu, 27 Oct 2022 00:37:27 +0000 |
parents | 3ab9d37e547e |
children |
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## 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 ```