which assembler shoud i use after mapping with BWA

[volavii]

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?

[krobison]

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)

[volavii]

thanks krobison