Run ABYSS for single-ended reads

Question

[Kate]

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.

[shammond]

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:

abyss-pe k=63 se=run.fastq name=prefix "unitigs"

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.

[Sej Modha]

Abyss single end assembly commands are available on the wiki ABySS wiki

[Kate]

Yes, that was where my command coming from. Still trying to get more familiar with abyss

[Kate]

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.

[Kate]

This is the code that used --

ABYSS -k63 run.fastq -o run_abyss_dnv63k_contigs.fa

Any comments or suggestions? Thank you in advance!

Answer 1

[Kate]

Actually I am trying to see if there are any other options from abyss can help to increase the contig length. Any suggestions are welcome!

[Sej Modha]

Use multiple k-mers in ABySS.

[Kate]

I tried looping different kmers and all have similar max lengths of contigs