Alignment Visualization

[kwtennis311]

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?

Thanks

[jgibbons1]

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.

[maubp]

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?

http://www.sanger.ac.uk/resources/software/act/

[colindaven]

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.

[zee]

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

[Rao]

mummer may be best option