Run ABYSS for single-ended reads
Hello,
I just run some abyss denovo with different kmers for single ended reads. However when I used abyss-fac to check, all the other parameters showed 0 except the n, example as below. Anyone has any ideas why is this?
n n:500 n:N50 min N80 N50 N20 E-size max sum name
111107 0 0 0 0 0 0 0 0 0 contig.fa
Thank you in advance.
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This is the code that used --
Any comments or suggestions? Thank you in advance!
Hi Kate, Those abyss-fac results mean that all of the contigs were shorter than 500 bp, and since its default behaviour is to report the stats on contigs >= 500, all the other stats are 0. You can change this length cut-off with the -t option.
Even without pairing information, you should be able to assemble contigs larger than this.
Try this command instead:
This will halt the assembly after the unitigs stage, since pairing information is required to assemble contigs. Your output file will be called prefix-3.fa.
Abyss single end assembly commands are available on the wiki ABySS wiki
Yes, that was where my command coming from. Still trying to get more familiar with abyss
Thank you for the input. I use -t to set the cutoff as 100 and it did have non-zero values for the contig file, however the max length showed less than 300bp, which seems not a good assembly.
I also tried the command that you suggested, it gives the same max length of contig.