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Last pushed: 5 days ago
Short Description
bowtie2
Full Description

bowtie2

bowtie2 license: GPLv3

Useful Links

Example Usage

See the container github-site for further usage documentation.

To start a container

docker run -it comics/bowtie2 bash

Following the bowtie2 usage example from the official bowtie2 MANUAL:

BT2_HOME=/software/applications/bowtie2/v2.2.9/
bowtie2-build $BT2_HOME/example/reference/lambda_virus.fa lambda_virus
bowtie2 -x lambda_virus -U $BT2_HOME/example/reads/reads_1.fq -S eg1.sam
bowtie2 -x lambda_virus -1 $BT2_HOME/example/reads/reads_1.fq -2 $BT2_HOME/example/reads/reads_2.fq -S eg2.sam
bowtie2 --local -x lambda_virus -U $BT2_HOME/example/reads/longreads.fq -S eg3.sam
bowtie2 -x $BT2_HOME/example/index/lambda_virus -1 $BT2_HOME/example/reads/reads_1.fq -2 $BT2_HOME/example/reads/reads_2.fq -S eg2.sam
samtools view -bS eg2.sam > eg2.bam
samtools sort eg2.bam eg2.sorted
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comics
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