Question: Audit trail for Bioinformatics software tools
gravatar for kspata
10 days ago by
kspata40 wrote:


I analyze several samples every day for variant analysis using align to reference method. For this purpose I use different Bioinformatics software such as Bowtie2/BWA, Samtools, and Freebayes. Is there a way in which I can know which version of software was used to process a particular sample. This should work like an audit trail, informing say Sample1 was aligned using bowtie2 vX.X.X, Sample2 was analysed using Bowtie2 vX.X.Y, and so on.

For example

bowtie2 --version command gives the output of Bowtie2 installed on the system as follows:

/usr/local/bin/bowtie2-align-s version 2.2.2

another approach,

samtools view -H sample.sorted.bam

@HD VN:1.0 SO:coordinate @SQ SN: reference LN: @PG ID:bowtie2 PN:bowtie2 VN:2.2.2 CL:"/usr/local/bin/bowtie2-align-s --wrapper basic-0 -x -I 0 -X 1000 --fr -p 16 --local --passthrough -1 /tmp/40466.inpipe1 -2 /tmp/40466.inpipe2"

Both these commands do not tell that Sample1 was processed using bowtie2, Sample2 was processed using Bowtie2 and so on.

I would like to get an audit trail, where I will know for each software which version was used to process which sample.


ADD COMMENTlink written 10 days ago by kspata40

You could capture this information (bowtie2 --version) in your analysis master logs for projects. Unix command script can capture all interactive dialog from a terminal sessions. Standard error and standard output logs captured from the analysis should include this information and can be saved.

You could also use a workflow system like snakemake to capture/automate your interactions and log those actions.

ADD REPLYlink modified 10 days ago • written 10 days ago by genomax60k
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