Question: Is Bcbio-nextgen software good for the whole genome sequencing alignment and variant calling, are there any alternatives?
0
gravatar for vassialk
5.0 years ago by
vassialk190
Belarus
vassialk190 wrote:

Is Bcbio-nextgen software good for the whole genome sequencing alignment  and variant calling, are there any alternatives? Can it accept a contig and a whole genome reference as an input?

sequencing wgs software • 1.6k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by vassialk190
3

This is an extension of What open source alignment software, variant callers are most appropriate for the whole genome experiments? - I think you could have appended your specific queries to your original question.

There are plenty of alternatives from 'roll your own' to 'buy a commercial package' - this line of questioning is not specific enough to generate useful answers.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Daniel Swan13k
1
gravatar for DG
5.0 years ago by
DG7.1k
DG7.1k wrote:

Bcbio-nextgen was designed to go from raw output of sequencing (FastQ's or raw data from the sequencing machine before demultiplexing, etc) and take it through short-read mapping, variant calling, annotation, etc. I don't think it has wrappers for any alignment tools that work with contigs or longer sequences but I could be wrong. What kind of data re you working with if you already have contigs?

ADD COMMENTlink written 5.0 years ago by DG7.1k
0
gravatar for vassialk
5.0 years ago by
vassialk190
Belarus
vassialk190 wrote:

Tuberculosis WGS --- contigs and reference annotated .gb files, thx

ADD COMMENTlink written 5.0 years ago by vassialk190
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