Public | Automated Build

Last pushed: a year ago
Short Description
bowtie2 v2.2.9 on Centos7
Full Description

bowtie2-2.2.9

bowtie2-2.2.9 license: GPLv3

Useful Links

Example Usage

See the container github-site for further usage documentation.

To start a container

docker run -it sglim2/bowtie2-2.2.9 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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Owner
sglim2
Source Repository

Comments (2)
sglim2
a year ago

@sletort: Yes, they are there in the PATH. These are all available in the path:

  • bowtie2
  • bowtie2-align-l
  • bowtie2-align-s
  • bowtie2-build
  • bowtie2-build-l
  • bowtie2-build-s
  • bowtie2-inspect
  • bowtie2-inspect-l
  • bowtie2-inspect-s

But I'll update the documentation and give examples.

sletort
a year ago

None of the bowtie2 executables are in the PATH.
It is not obvious to use them from their install dir.