Question

Whole Genome Seq Analysis Software for Identifying Specific Gene Variants

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3.5 years ago

dk0319 ▴ 70

What are some of the popular free software tools for analyzing whole genome sequencing data? I am particularly interested in analyzing the sequences that map to a particular gene region in order to confirm predicted variation in the sequence. So if anyone as any recommendations, I am very interested to hear them, as I have never done WGS analysis before, only RNA-seq.

next-gen sequencing • 605 views

ADD COMMENT • link updated 3.5 years ago by swbarnes2 14k • written 3.5 years ago by dk0319 ▴ 70

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what did you find so far ?

ADD REPLY • link 3.5 years ago by Pierre Lindenbaum 161k

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I have used commercial like CLC and snapgene in the past. As for free there is star, bowtie and Rsubread. But, I use those for RNA-seq not WGS. And none of them provide a visual map, apart from the commercial, at least as far as I know.

ADD REPLY • link 3.5 years ago by dk0319 ▴ 70

score 2 · Accepted Answer · 2020-10-01

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3.5 years ago

swbarnes2 14k

If all you want to do is look at one gene, I'd eyeball it in IGV. Any aligner that works with RNASeq will work fine for DNA, and the indexed bam can be read into IGV.

https://software.broadinstitute.org/software/igv/download

ADD COMMENT • link 3.5 years ago by swbarnes2 14k