SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Contig length, k-mer coverage, and differential expression nbogard General 3 09-10-2013 11:30 AM
Velvet Assembler: expected coverage versus estimated coverage versus effective covera DMCH Bioinformatics 1 11-30-2011 04:21 AM
ABySS contig coverage? jgibbons1 Bioinformatics 2 09-24-2010 06:56 AM
solid_denovo_postprocessor.pl removes velvet contig sequence. KevinLam Bioinformatics 0 02-09-2010 05:04 PM
How quantitative is contig coverage? AlexB 454 Pyrosequencing 4 09-11-2009 02:38 AM

Reply
 
Thread Tools
Old 09-16-2010, 06:21 AM   #1
genelab
Member
 
Location: honston

Join Date: Nov 2009
Posts: 27
Default Get coverage of each site on contig generated by Velvet

Hello everyone,
I am now working with velvet denove assemly of my short reads data. The result directory contains the following files (contigs.fa Graph2 LastGraph Log PreGraph Roadmaps Sequences stats.txt velvet_asm.afg). I want to get the depth of coverage of each site on contig sequences contained in "contig.fa". Is the coverage information contained in "velvet_asm.afg" file?
Any suggestion will be very appreciate!
genelab is offline   Reply With Quote
Old 09-16-2010, 06:38 AM   #2
Zigster
(Jeremy Leipzig)
 
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116
Default

that should be in the deflines
>NODE_1_length_563_cov_201.866791

201.866791 is the kmer coverage Ck (read kmers per contig kmers)

if you know your average read length you can convert to get x-coverage (read bp per contig bp)

Cx=Ck*L/(L-k+1)

where k is your kmer setting and L is your read length
so if I used a kmer of 37 and an average read length of 50
Cx=202*50/(50-37+1)=721X

if you want depth on a base pair granularity you are probably best off realigning and using Samtools
__________________
--
Jeremy Leipzig
Bioinformatics Programmer
--
My blog
Twitter
Zigster is offline   Reply With Quote
Old 09-16-2010, 10:37 PM   #3
Torst
Senior Member
 
Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275
Default

Quote:
Originally Posted by genelab View Post
I am now working with velvet denove assemly of my short reads data. The result directory contains the following files (contigs.fa Graph2 LastGraph Log PreGraph Roadmaps Sequences stats.txt velvet_asm.afg). I want to get the depth of coverage of each site on contig sequences contained in "contig.fa". Is the coverage information contained in "velvet_asm.afg" file?
If I understand correctly, you want the depth of read coverage at each nucleotide position in the genome?

Velvet does not produce this. However, the .afg file contains, for each read, where it is in a contig. You could use this to build a "coverage" report. I suspect AMOS might be able to do this for you. The software "Tablet" can load the .afg file and will draw the coverage for you too.
Torst is offline   Reply With Quote
Old 09-18-2010, 12:51 AM   #4
genelab
Member
 
Location: honston

Join Date: Nov 2009
Posts: 27
Smile

Quote:
Originally Posted by Torst View Post
If I understand correctly, you want the depth of read coverage at each nucleotide position in the genome?

Velvet does not produce this. However, the .afg file contains, for each read, where it is in a contig. You could use this to build a "coverage" report. I suspect AMOS might be able to do this for you. The software "Tablet" can load the .afg file and will draw the coverage for you too.
Yes, my purpose is to get the depth of read coverage at each nucleotide position in the contig generated by Velvet. Thanks for your great suggestion, I will try it.
genelab is offline   Reply With Quote
Old 09-18-2010, 01:25 AM   #5
genelab
Member
 
Location: honston

Join Date: Nov 2009
Posts: 27
Default

Quote:
Originally Posted by Zigster View Post
that should be in the deflines
>NODE_1_length_563_cov_201.866791

201.866791 is the kmer coverage Ck (read kmers per contig kmers)

if you know your average read length you can convert to get x-coverage (read bp per contig bp)

Cx=Ck*L/(L-k+1)

where k is your kmer setting and L is your read length
so if I used a kmer of 37 and an average read length of 50
Cx=202*50/(50-37+1)=721X

if you want depth on a base pair granularity you are probably best off realigning and using Samtools

Zigster,
thanks for your great help!

genelab
genelab is offline   Reply With Quote
Old 08-03-2013, 10:40 PM   #6
diptarka
Member
 
Location: DDN

Join Date: Mar 2013
Posts: 10
Default

Hi, all
I am new to denovo genome assembly. I have a fastq sequence data which i have to assemble using velvet. I used the velvet optimiser script with different hash length from 27 to 41 and it predicted best to be 37. The output file contigs.fa contains 260 contigs whereas log file predicts 283 nodes, where are the rest gone? Length given in contigs.fa is in k mers? how do i calculate it's actual nucleotide length in bp?. How do i understand whether the assembly is good or bad. FInal stat given after script running:
Final graph has 283 nodes and n50 of 347, max 2336, total 68614, using 19064/50000 reads
Why are the number of used reads so low?
diptarka is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO