Generating input for Amosvalidate

[flobpf]

Hi,

I'm using ABySS to assemble 14 FASTQ PE files into a 300MB assembly. I wanted to use AmosValidate (http://bit.ly/pSVBr8) for validation since, as far as I know, it is the only tool available out there (pls correct me if i'm mistaken). However, ABySS does not provide a way of creating an ACE/AFG output to be used as an input for toAmos (tool deprecated).

I have also mapped all my Illumina reads to the assembly giving me a SAM file.

Some people suggested using Galaxy for conversion of SAM to ACE, but Galaxy doesnt provide this functionality. Nor does SAMtools. I wonder if there is a good way of generating the input files for Amosvalidate using the files I have?

Thanks

[maubp]

I have also mapped all my Illumina reads to the assembly giving me a SAM file.

That isn't the same thing as the original assembly, it would just be a collection of pairwise alignments of the reads onto the contigs.

It may not be possible to get the original read placement used from ABySS.

[flobpf]

Abyss protocol

Hi Maubp,

Thanks for the reply. I did bowtie because the tool abyss2afg/abyss2ace use Kaligner to align reads to the contigs and pass the output to abyss2afg. The command suggested is:

$ abyss2afg --help
Usage:
    KAligner --seq -mk K reads.fa contigs.fa | abyss2afg contigs.fa -
    >out.afg

    bank-transact -cb out.bnk -m out.afg

    hawkeye out.bnk

I agree the mapping may not be the same as what ABySS finally ended up using. I used bowtie because there I could explicitly define PE reads with the -1 and -2 flags.

An alternate approach would be fine too.