Abyss @ 454

[joa_ds]

Hi there,

Is ABYSS designed for assembly of 454 reads?


# ./ABYSS -k25 -o /data/454/data/_Test_assembly /data/454/data/2.TCA.454Reads.fna

gives me the following

2.TCA.454Reads.fa' is an unknown format
Expected either `>' or `@' or 11 fields
and saw `C' and 1 fields

?

[ekg]

Interestingly, I am having the same issue. As a sanity check I'm attempting to reassemble some contigs produced by ABySS. I'm not sure what the parser expects to read and the error message doesn't print the location of the error in the file.

[ekg]

Also, you should write an email to the ABySS-users list. The authors of ABySS read the list and are very helpful.

[flxlex]

Looks like ABYSS expects a fastq formatted file, while your file is fasta formatted:

http://en.wikipedia.org/wiki/FASTQ_format
http://en.wikipedia.org/wiki/FASTA_format