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Old 06-15-2010, 07:23 AM   #1
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Default Alignment Visualization

I am looking for a way to align contigs from a de novo assembly against a reference genome and visualize which parts of the genome are covered. Any recommendations?

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Old 06-15-2010, 08:27 AM   #2
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I really like Tablet (http://bioinformatics.oxfordjournals...t/btp666v1.pdf) as a genome viewer. I believe it supports ACE, AFG, MAQ, SOAP and SAM formats.
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Old 06-15-2010, 09:27 AM   #3
Peter (Biopython etc)
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But Tablet is for viewing individual contigs from assemblies on their own (looking at the reads within a contig).

The question was about comparing the contigs of an assembly against a reference genome. This has similarities to comparing different genomes... maybe ACT (the Artemis Comparison Tool) would be suitable?
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Old 06-16-2010, 06:38 AM   #4
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We used BLASTn to map ca 2000 contigs against various references.
Visualisation of contig position and the annotated genes in that region was with the R package GenomeGraphs.

I would really recommend this and can send an example script if you pm me with your email address.
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Old 06-16-2010, 09:18 PM   #5
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What is your average contig length? For contigs assembled from short reads I have been using " bwa bwasw"

It natively produces SAM format which your can convert to BAM and directly view in Tablet/IGV
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Old 06-17-2010, 12:04 AM   #6
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mummer may be best option
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