Small Genome Mapping Assembly
Hi,
Can anyone suggest me a good small genome assembly with reference. My sequence are produced from sanger sequencing.
Thanks,
N.
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Ram
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Nicolas Rosewick
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Nicolas Rosewick
5 answers
I suggest MIRA.
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Martin A Hansen
You could try Consed in http://www.phrap.org/phredphrapconsed.html . This tool was used during the SRAS outbreak: http://www.sciencemag.org/content/300/5624/1399.long
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Pierre Lindenbaum
This is a program we have developed at the CVR for assembling viral genomes: http://bioinformatics.cvr.ac.uk/Tanoti/index.php
It is specifically designed to map as many reads as possible and allows for quite a lot of variation relative to the reference.
Are your sequences in fastq format?
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Ram
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Joseph Hughes
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What kind of genome ?
It's a virus genome so it's very small ~10kb
I assume you mean "assembler" not "assembly"? And by "reference" you mean literature, not a reference genome?
Yes assembler sorry. And by reference I mean reference genome