velvet

[bioenvisage]

hi After running velvet assembly I got Estimated Coverage = 25.12000
Estimated Coverage cutoff = 10.250000
Final graph has 11106 nodes and n50 of 498, max 13308, total 243547, using 221137/2500000 reads, so I have 3 questions here.

1) what does this max 13308 ( It is the maximum contig length obtained)
2)what does this total 243547 refers to?
3) should I run the velvet again by using the obtained estimated cov cutoff and estimated coverege (for eg here should I run velvet again using cov_cutoff 10
est_coverege 25)

can any one answer this???

thanks

[lcollado]

1) Yes, it's the length of the longest contig you got.
2) It's the sum of the length of all your contigs.
3) You should probably try out the velvetOptimizer.pl script that is distributed along Velvet. Or you can join the Velvet mailing list and ask there.

[Zigster]

using 221137/2500000 reads

that is a very low read usage - i would focus on figuring out why so few of your reads are making it into the assembly. Maybe they need to be trimmed further?

[bioenvisage]

hi zingster thnx for ur reply ...but my read length is 75 bp, do u think it should be trimmed further.

[Zigster]

Trim on quality, not length
Joseph Fass's script does soft trimming - try 10, 15, and 20

http://wiki.bioinformatics.ucdavis.edu/index.php/TrimBWAstyle.pl