Repeat Masking Of Gene Enriched Genomic Reads On 454 Platform

Question

[User 9042]

hi,

i have sequenced gene enriched genomic reads on 454 platform. After removing reads of organeller genome, i want to assemble the filtered reads on gsAssembler. Being genomic reads, should i repeat mask it prior to assembly? Whether gsAssembler can assemble repeat masked reads?

KM (India)

Answer 1

[Damian Kao]

There is a detangling phase during Newbler assembly that will sometimes just hang for a long time. If you find that happening, one possibility is that there is a large amount of repeats in your organism and Newbler is having a tough time resolving them into contigs.

This is a repeat question of [?]this[?] by the way.

[User 9042]

but the difference is of genomic reads..

Answer 2

[SES]

I would recommend first using BLAST or RepeatMasker and a library of repeats from a closely related species to assess the level of repetitive sequences in your enriched library. This will also tell you how well the treatment worked if you have some shotgun data for comparison. I have analyzed reduced representation libraries where the treatment was effective at removing 90% of the transposon sequences, but if you want just the gene sequences, that may not be enough.

If you really want to remove the repeats then you could remove them using a library of repeats from a closely related species (or the species of interest, if a repeat library exists). I would not try to mask and then assemble because it is not clear to me how Newbler will treat those reads (I doubt it would falsely assemble the masked regions, but it may just skip those reads altogether anyway).