Question: Converting Blast Output To Sam Format
5
gravatar for Wen.Huang
5.8 years ago by
Wen.Huang1.1k
Wen.Huang1.1k wrote:

Hi everybody,

I was wondering if there is a blast output parser that convert blast output to SAM format. There are many blast parser out there, but most for compressing results to more readable statistics. I would appreciate if anybody can point me to something that extracts the alignments.

Thanks!

sam blast parser • 6.7k views
ADD COMMENTlink modified 3.0 years ago by Pierre Lindenbaum108k • written 5.8 years ago by Wen.Huang1.1k
1

The NCBI seem to be working on adding SAM output to BLAST+ directly, see http://blastedbio.blogspot.co.uk/2015/07/ncbi-working-on-sam-output-from-blast.html

ADD REPLYlink written 2.8 years ago by Peter5.6k

http://www.biostars.org/post/show/13449/

ADD REPLYlink written 5.7 years ago by Rm7.7k
7
gravatar for Istvan Albert
5.8 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

The samtools source distribution contains a file called misc/blast2sam.pl that can convert the output of earlier versions of blast (use a blast release from around 2007). In the meantime the blast output has changed in subtle (and undocumented) ways, Heng Li has stated that this blast converter is not being maintained to operate for current versions of blast.

ADD COMMENTlink written 5.8 years ago by Istvan Albert ♦♦ 77k
7
gravatar for Pierre Lindenbaum
3.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum108k wrote:

(2.8 years later:) I asked my student to write a blastn to sam converter. His C code is available at : https://github.com/guyduche/Blast2Bam

ADD COMMENTlink written 3.0 years ago by Pierre Lindenbaum108k
1

awesome! there are so many BAM file visualizers out there and none (that I know of ) for BLAST output

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 77k
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