Question: Velvet Raw Seq Assembler
0
gravatar for tanjafiegel
7.1 years ago by
tanjafiegel40
UK -- NCL
tanjafiegel40 wrote:

To assemble fastq raw seq read from Ion Torrent for bac genome (3Mb), what are the 'best' commands to get the optimum contig alignment on average (velveth and velvetg).

read ion-torrent velvet assembly • 2.7k views
ADD COMMENTlink modified 6.8 years ago by Leszek4.0k • written 7.1 years ago by tanjafiegel40

this might be a helpful link to get you started: http://dna.med.monash.edu.au/~torsten/velvet_advisor/

ADD REPLYlink written 7.1 years ago by Simon Cockell7.3k
3
gravatar for Leszek
7.1 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

You can try Newbler or Mira

ADD COMMENTlink written 7.1 years ago by Leszek4.0k

Newbler seems to work the best for me so far, for Ion Torrent. VelvetOptimiser worked OK. On a recent de novo assembly with Newbler I got 465 contigs, N50: 17kb, and an assembly size of 4.1 Mb. With VelvetOptimiser, I got 1480 contigs, 3.9 Mb, and N50: 4kb. When I merged with the combiner in CG-Pipeline (which uses Minimus2), I got a final assembly of 454 contigs, N50: 19.5 k, and a genome length of 4.2 Mb.

I have not tried Mira for Ion Torrent and so I cannot comment on that.

ADD REPLYlink written 7.1 years ago by Lee Katz2.9k
0
gravatar for Jeremy Leipzig
7.1 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

i don't think velvet would be good for "homopolymer-ish" data. it is bad for 454 and it behaves even worse for ion torrent.

http://pathogenomics.bham.ac.uk/blog/2011/05/first-look-at-ion-torrent-data-de-novo-assembly/

ADD COMMENTlink written 7.1 years ago by Jeremy Leipzig18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1872 users visited in the last hour