Large scale alignment and other related tasks

[fahmida]

Good day everyone,

I've nearly 2GB genomic data of a newly assembled genome in nearly 1 million scaffolds.
Also I've a 100MB 454 reads (average read length ~350nt).
I would like to align/map all the 454 reads against the scaffolds and view it in an alignment viewer. The objective is to find and extract those scaffold regions which have highest number of 454 reads aligned to it.

Any particular tool/code/pipeline/suggestions will be greatly appreciated.

Regards.

[flxlex]

If you have access, gsMapper (newbler from 454) will do the job. Check the 454AlignmentInfo file for a per-base mapping count (coverage), or the 454RefStatus file for a per-scaffold coverage. If you specify the ace-file output you should be able to view the results in Tablet or other viewers.

[zee]

There are some alternatives to gsMapper, such as

*bwa's bwa-sw
*Mosaik
*Novoalign (decrease gap open/extend penalties)

Choose a tool with SAM/BAM output format so getting it into a viewer will be easy. Viewers of choice would be

*IGV
*IGB
*Tablet