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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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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 -
FWIW, bowtie can handle fasta files as well. Just use the '-f' option:Originally posted by zhidkov.ilia View Post
Code:bowtie-build -f contigs.fa contig_bowtie bowtie --sam -f contig_bowtie reads.fa
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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.
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.Comment
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