Velvet and coverage range

[BoggyP]

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

[seb567]

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.