Hellow fellows,
I've been assembling a genome of a snake with SOAPdenovo using big set of paired-end reads that were sequenced in Illumina hiScan.
I already made a lot of assemblies tuning the parameters and using filtered/non-filtered reads, but I'm always getting a low contig N50 of 1.4k (against >30k on references).
I've read something about breaking the scaffolds in contigs and using the reads again to map one end to the gap but I couldn't find a detailed explanation on how to do that. The fact is that in all assemblies that took this approach they could extend contigs lengths and N50 as a consequence.
Could someone recommend me a text to read about that? has any of you ever done this?
Also, another doubt I have is regarding evaluating scaffolds with QUAST (http://quast.bioinf.spbau.ru/manual.html)... I see it analyzes the scaffold file in two ways, and one of them gives me a bigger N50 (i.e. 3.5k) but I don't know the differences between the two results quast gives me.
No problem when evaluating contigs though.
Any clues here too?
Thanks a lot in advance!
Condomitti.
I've been assembling a genome of a snake with SOAPdenovo using big set of paired-end reads that were sequenced in Illumina hiScan.
I already made a lot of assemblies tuning the parameters and using filtered/non-filtered reads, but I'm always getting a low contig N50 of 1.4k (against >30k on references).
I've read something about breaking the scaffolds in contigs and using the reads again to map one end to the gap but I couldn't find a detailed explanation on how to do that. The fact is that in all assemblies that took this approach they could extend contigs lengths and N50 as a consequence.
Could someone recommend me a text to read about that? has any of you ever done this?
Also, another doubt I have is regarding evaluating scaffolds with QUAST (http://quast.bioinf.spbau.ru/manual.html)... I see it analyzes the scaffold file in two ways, and one of them gives me a bigger N50 (i.e. 3.5k) but I don't know the differences between the two results quast gives me.
No problem when evaluating contigs though.
Any clues here too?
Thanks a lot in advance!
Condomitti.
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