puzzled by ABYSS README

[anyone1985]

I would like to use varous softwares to assemble my solexa data. The ABYSS Readme puzzled me that I don't know how to set the parameter of lib in the program of abyss-pe.

http://www.bcgsc.ca/platform/bioinfo/software/abyss

for example, My data is marked by
@Minna_FC18_PE:4:1:624:594/1
+Minna_FC18_PE:4:1:624:594/1
@Minna_FC18_PE:4:1:624:594/2
+Minna_FC18_PE:4:1:624:594/2

What should I set the parameter of lib?

[sjackman]

The abyss-pe driver script does not currently support assembling FASTQ files, although each of the programs that it calls does. This limitation is something that I hope to fix in the near future. In the mean time, you may find it easiest to convert your FASTQ files to FASTA (with a .fa filename extension). If your file of FASTA reads is named ecoli-reads.fa, you would set lib=ecoli-reads

If you are handy with editing Makefile scripts, you could modify the abyss-pe driver script (only 74 lines) to support FASTQ files with whichever extension you prefer.

Cheers,
Shaun

[Haneko]

Hi sjackman,

I saw from another post you are one of the authors for ABYSS. I'm having some trouble using the mailing list, for some reason my emails keep bouncing back. I'm new to it so I could be using it wrongly.

I’m using ABYSS for assembly of Solexa paired-end 76bp reads. The reads supposedly come from a particular region of the human genome, and I’m trying to assemble all these reads to hopefully map them back to the region of interest. This is the first time I’m using ABYSS, so I’m not sure about a lot of things.

I was reading the ABYSS paper and it said that “alternative sequences are retained in a log file”. May I know where this log file is? What are these “alternative sequences”?

I’m also assuming that the file –contigs.fa is the final file I should be looking at for all the contigs assembled, and to be mapped back to the genome. Is that correct? There are quite a few -<number>.fa files as output, I’m not sure what each file holds.

From SeqWIKI:

“A fourth column will be present for paired-end contigs (scaffolds) and is the list of single-end contig IDs that compose that paired-end contig (scaffold). If you suspect a misassembly, it can be informative to look at the single-end contigs.”

Where do I find these single-end contigs? I can’t find them in my –contigs.fa file using the contig IDs given.

Any help will be greatly appreciated!!

[sjackman]

Hi Haneko,

The ABySS mailing list has moved to Google Groups:

http://groups.google.com/group/abyss-users

The alternative sequences are stored in bubbles.fa. They represent heterozygous variation and collapsed repeats.

The single-end contigs are stored in ${name}-4.fa. The other numbered FASTA files are intermediate stages of the assembly.

Cheers,
Shaun

[Haneko]

Hi Shaun,

Many thanks!