which assembler shoud i use after mapping with BWA

volavii

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Join Date: Apr 2013

Posts: 16
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#1

which assembler shoud i use after mapping with BWA

07-03-2013, 04:25 AM

Hey

i want to assemble my reference mapped reads (BWA2) into a consesus sequence...
Is there a programm or do i have to write a script?
Tags: assembly consensus, bwa
krobison

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Join Date: Nov 2007

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#2

07-03-2013, 05:43 AM

Second Google hit for "consensus sequence from bam"

http://chipster.csc.fi/manual/samtools-consensus.html

which gives this command

samtools mpileup -uf reference.fa alignment.bam | bcftools view -cg - | vcfutils vcf2fq

(requires samtools, vcftools, vcftools)
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volavii

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Posts: 16
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#3

07-03-2013, 06:47 AM

thanks krobison
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