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Old 12-19-2010, 01:45 PM   #1
harrb
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Location: Germany

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Default absolute k-mer coverage explained (Abyss)

The (very limited) Abyss manual explains the fasta headers in the contigs assembly outfile like this:


>n iii jjjj
Where n is the numeric contig ID, iii is the contig length in nucleotides, and jjjj is the absolute k-mer coverage.

I don't understand what "absolute k-mer coverage" means. Can someone maybe explain? But what I would really like to know is which basepair in a contig are represented by how many reads. IS there a way to get this from the k-mer coverage?

THANKS
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Old 12-21-2010, 02:01 PM   #2
boetsie
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Default

Hi harrb,

have a look at this older thread about the header;
http://seqanswers.com/forums/showthr...abyss+coverage

About the coverage (per position on the contig i think you mean?) you can probably run ABYSS with the option

--coverage-hist=FILE

This option (as stated at http://seqanswers.com/wiki/ABySS) records the k-mer coverage histogram in FILE. Though, I'm not 100% sure, since i can not test it @tm .

Otherwise, you can map your reads to the contigs (Bowtie, BWA), producing a .sam file. Convert the .sam file to .bam file and do;

samtools pileup -f your_ref.fa your.bam

Have a look at this thread;

http://seqanswers.com/forums/archive...hp/t-7679.html

Good luck,
Boetsie
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