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Old 07-23-2011, 06:00 PM   #1
ojy
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Location: California

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Default Align reads to contigs

I need to align reads to contigs (both in fasta format). Preferably with visualization. I will appreciate suggestions of tools which can do this.
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Old 07-24-2011, 12:14 AM   #2
zhidkov.ilia
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Hi ojy,
you can try use Sequencher (http://genecodes.com/?referrer=20yea...FYdH3godv0BYyQ), in this case you will have mapping and visualization (use the demo version see if it fits your needs).
Another approach is to turn your reads from fasta to fastq (http://en.wikipedia.org/wiki/FASTQ_format),just stick them (reads) quality of 30 for each base and then you can use aligners for NGS (such as bowtie (http://bowtie-bio.sourceforge.net/index.shtml), bwa (http://bio-bwa.sourceforge.net/bwa.shtml) and then visualize your results with IGV-viewer (http://www.broadinstitute.org/igv/v1.2).

Ilia
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Old 07-25-2011, 08:55 AM   #3
gringer
David Eccles (gringer)
 
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Quote:
Originally Posted by zhidkov.ilia View Post
Another approach is to turn your reads from fasta to fastq, just stick them (reads) quality of 30 for each base and then you can use aligners for NGS and then visualize your results with IGV-viewer (http://www.broadinstitute.org/igv/v1.2).
FWIW, bowtie can handle fasta files as well. Just use the '-f' option:

Code:
bowtie-build -f contigs.fa contig_bowtie
bowtie --sam -f contig_bowtie reads.fa
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Old 07-25-2011, 09:16 AM   #4
john1923
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I use Bowtie as gringer suggested.

Then Tablet to view the sam file. It shows it as a big alignment that you can scroll though.

http://bioinf.scri.ac.uk/tablet/

If you're a biologist (like me) it's worth seeing if your uni has an administered central bio-informatics server that you can use. Having someone else install everything is a massive help.
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