Question: Whole Genome Sequencing (WGS) Alignment Quality check softwares/tools
1
gravatar for ravi.uhdnis
4.3 years ago by
ravi.uhdnis170
United States
ravi.uhdnis170 wrote:

Hi,

I use BWA to align my WGS human data reads from illumina HiSeq2500 machine against GRCh38 as reference genome. Although BWA provide certain basic information about the mapping done (e.g. % of mapped reads etc) but Is there any software/tools which can provide me such information in greater details, kind of overall alignment quality matrix ?.

ADD COMMENTlink modified 4.2 years ago • written 4.3 years ago by ravi.uhdnis170
2
gravatar for Brian Bushnell
4.3 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

BBMap supports extensive quality-related output histograms.  For example:

bbmap.sh ref=hg19.fa in1=read1.fq in2=read2.fq mhist=mhist.txt ihist=ihist.txt ehist=ehist.txt qhist=qhist.txt qahist=qahist.txt indelhist=indelhist.txt

...and various others.  That will generate the files mhist.txt, which shows the rates of match, substitution, insertion, deletion, and N at each base position; ihist, the insert size histogram; and so forth (they're documented in the shellscript).  They're all tab-delimited columns, so they're easy to plot in R or Excel.

ADD COMMENTlink written 4.3 years ago by Brian Bushnell17k
1
gravatar for ravi.uhdnis
4.2 years ago by
ravi.uhdnis170
United States
ravi.uhdnis170 wrote:

Thank you Guys. I found "Qualimap (http://qualimap.bioinfo.cipf.es/)" is a good software for knowing the quality of Alignment run. The reference article is here ("http://www.ncbi.nlm.nih.gov/pubmed/22914218"). 

ADD COMMENTlink written 4.2 years ago by ravi.uhdnis170
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