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Old 05-26-2011, 10:50 AM   #1
BoggyP
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Location: Toronto

Join Date: May 2011
Posts: 1
Default Velvet and coverage range

Hi!

I'm running velvet on short paired reads at various kmer lengths with, for example:
./velvetg output_148/ -ins_length auto -exp_cov auto -read_trkg yes -amos_file yes

I saw in the log that it stores 'Median coverage depth' but does it store the coverage range anywhere?

Thanks,
BoggyP
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Old 05-31-2011, 09:46 AM   #2
seb567
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Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
Default

Quote:
Originally Posted by BoggyP View Post
Hi!

I'm running velvet on short paired reads at various kmer lengths with, for example:
./velvetg output_148/ -ins_length auto -exp_cov auto -read_trkg yes -amos_file yes

I saw in the log that it stores 'Median coverage depth' but does it store the coverage range anywhere?

Thanks,
BoggyP

What do you mean by coverage range ?

I guess you mean the frequency for each coverage depth value -- example: http://postimage.org/image/1p5t8wmsk/

If it is the case, the Ray assembler generates this kind of output file automatically.

http://denovoassembler.sf.net

Commands to achieve that:

Installation

wget http://sourceforge.net/projects/deno...-1.4.0.tar.bz2
tar xjf Ray-1.4.0.tar.bz2
cd Ray-1.4.0
make

Assembly

mpirun -np 8 code/Ray -k 21 -p forward.fastq reverse.fastq -o RayAssemblyTest

Analysis

ls RayAssemblyTest.*
less RayAssemblyTest.CoverageDistribution.txt
./scripts/plot-coverage-distribution.R RayAssemblyTest.CoverageDistribution.txt
ls RayAssemblyTest.CoverageDistribution.txt.pdf

p.s. I am the author of Ray.
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