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Old 11-15-2010, 07:30 PM   #1
ketan_bnf
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Default Can MAQ be used for 454 sequencing data for SNP detection?

hello,


I am having 454 sequencing data from which i am trying to find SNPs. Can MAQ do that thing for me, I know that it is mostly used for SOLEXA sequence reads, but anyone have ever tried with 454 sequencing data?

If yes, whether results are reliable?

Which from following softwares i choose, MAQ/MOSAIK/SAMtools?

Thanks.
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Old 11-16-2010, 03:02 AM   #2
colindaven
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Perhaps try Mosaik, Roche's GsAssembler, or Novoalign for alignment
then Samtools / Varscan for variant calling.

Maq is not appropriate for 454 in my experience
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Old 11-16-2010, 05:34 AM   #3
krobison
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I haven't tried it on 454 data (yet! perhaps today!) but the BWA package contains a mode (bwasw) for handling long reads.
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Old 11-16-2010, 06:45 AM   #4
drio
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Careful, from the bwa site:

Quote:
Does BWA align 454 reads?

Yes and no. The BWA-SW component of BWA works well on 454 reads about 200bp or longer. It achieves similar alignment accuracy to SSAHA2 while much faster. BWA-SW also works for shorter reads, but the sensitivity is lower. In addition, BWA-SW does not support paired-end alignment.
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Old 11-16-2010, 07:00 AM   #5
nickloman
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My strong recommendation is to use Roche's gsMapper (part of Newbler) for aligning 454 reads to a reference. It has specific handling for the 454 error model (homopolymeric tract errors, indels) which other aligners may not have.
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Old 11-16-2010, 07:30 PM   #6
ketan_bnf
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Thank you for your reply.
Right now i am trying with MOSAIK.

Which program should i use to convert sff to fasq, self_extract.py then fastaqual2fastq.pl or indraneil's sff2fastq?

Thanks
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