Question: (Closed) What software is designed for the microbe whole genome to whole genome alignment and accurate variant calling?
1
gravatar for vassialk
2.7 years ago by
vassialk150
Belarus
vassialk150 wrote:

What software is designed for the whole genome to whole genome alignment and variant calling? I have tried Ugene and NextGene and CLC. Need a more suitable solution. Thx.

ADD COMMENTlink modified 2.6 years ago by vranckx.katleen40 • written 2.7 years ago by vassialk150
1

nucmer and dnadiff from mummer. Pretty good on a few tries, though haven't carefully evaluate against other approaches.

ADD REPLYlink written 2.6 years ago by lh330k

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ADD REPLYlink written 3 months ago by Michael Dondrup44k
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gravatar for vranckx.katleen
2.6 years ago by
Belgium
vranckx.katleen40 wrote:

We have a software package, BioNumerics, designed specifically for this purpose for prokaryotic genomes. It can handle starting from the reads as well as from the assembled sequences. You can do SNP detection on mapped genomes, but also align de novo sequences and perform a mutation analysis on the aligned sequences. You can ask for a free trial to test it yourself. 

ADD COMMENTlink written 2.6 years ago by vranckx.katleen40
0
gravatar for h.mon
2.7 years ago by
h.mon15k
Brazil
h.mon15k wrote:

You would probably get more useful answers if you explained in more detail your data. I'll give two suggestions, under two different assumptions:

1) You have assembled genomes and no sequencing data: use Mauve, it aligns full and draft genomes and has a function to export SNPs.

2) You have Illumina sequencing data: use A5_MiSeq, it produces really goods assemblies, is easy to install and use. You could then use the BAM file it outputs to perform variant calling with SAMtools, there are lots of good tutorials around the web.

ADD COMMENTlink written 2.7 years ago by h.mon15k
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