Small Genome Mapping Assembly
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12.5 years ago

Hi,

Can anyone suggest me a good small genome assembly with reference. My sequence are produced from sanger sequencing.

Thanks,

N.

genome assembly mapping • 3.5k views
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What kind of genome ?

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It's a virus genome so it's very small ~10kb

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I assume you mean "assembler" not "assembly"? And by "reference" you mean literature, not a reference genome?

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Yes assembler sorry. And by reference I mean reference genome

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12.5 years ago

I suggest MIRA.

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12.5 years ago

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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12.5 years ago
Pasta ★ 1.3k

You can try Edena, it is very accurate and easy to use (you dont have tons of tools to install). And the developer is very nice :)

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12.5 years ago
Lee Katz ★ 3.1k

The AMOS package is really great for most things. Your question also depends on the chemistry you are using.

454 - Newbler continues to be the best at 454. Also, AMOScmp.

Illumina - Use Nesoni which is a nice wrapper around SHRiMP. Also, AMOScmp-shortReads

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9.7 years ago
Joseph Hughes ★ 3.0k

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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