Is Bcbio-nextgen software good for the whole genome sequencing alignment and variant calling, are there any alternatives?
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6.9 years ago
vassialk ▴ 200

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 software wgs • 2.0k views
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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.

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6.9 years ago
DG 7.3k

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?

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6.9 years ago
vassialk ▴ 200

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

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