yasir s - 2015-01-27

Hi

I ran SOAPdenovo on some paired end Illumina gDNA reads. I am interested in
the contigs. I looked at the .contig file and I see the descriptions have
something called cvg and tip. For example,

647 length 34 cvg_0.0_tip_0
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAT
and
39757045 length 7176 cvg_34.9_tip_0
AGAACAAGAATAAAAAGGAAACTATAAAACTAAAGCCCAAGAGAAATAGGATGCTAGGATGCTATGCTGCATCAAGTATCAAGTCCGTTTGCCTTGCTAG
...

Is cvg the coverage? Is it the average sequencing depth per base (i.e.,
normalized by contig length), or the number of reads aligning to the whole
contig?

Also, there are a whole bunch of short contigs with zero coverage. I am
assuming these don't show up in the scaffolds and should be thrown away
before any downstream analyses?

Thank you for your time.

 
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