Question: Run ABYSS for single-ended reads
0
gravatar for Kate
4.3 years ago by
Kate0
Kate0 wrote:

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.

assembly • 2.3k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Kate0

This is the code that used --

ABYSS -k63 run.fastq -o run_abyss_dnv63k_contigs.fa

Any comments or suggestions? Thank you in advance!

ADD REPLYlink modified 4.3 years ago by genomax89k • written 4.3 years ago by Kate0

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.

ADD REPLYlink written 4.3 years ago by shammond0

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

ADD REPLYlink written 4.3 years ago by Sej Modha4.7k

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

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Kate0

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.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Kate0
0
gravatar for Kate
4.3 years ago by
Kate0
Kate0 wrote:

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!

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Kate0

Use multiple k-mers in ABySS.

ADD REPLYlink written 4.3 years ago by Sej Modha4.7k

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

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Kate0
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