[AMOS-help] convert bam or sam format to afg or AMOS bank format

[d f <df6...@gm...>]

Hi,

Are there any plans on updating abyss-samtoafg (or samtoafg)
so that it can handle gapped alignments?

I have three assemblies (454/Newbler, Illumina/SGA, and
hybrid 454/Illumina/Newbler/SGA) that I would like to
compare using amosvalidate and FRCurve.  To assess
prevalence of collapsed repeats, I aligned my paired-end
reads with the longest fragment length (which are my 454
paired-end reads) to each assembly using SSAHA2, converted
the alignment output to AMOS bank format, and ran FRCurve.

To convert the SAM format to AMOS bank, I used
abyss-samtoafg and then ran bank-transact.  However, there
are short indels all over the alignments since the reads are
454. When I view the alignments in Hawkeye, the indels are
not handled properly. Indeed, Shaun Jackman, the author of
abyss-samtoafg, wrote that abyss-samtoafg does not handle
gapped alignments
(http://sourceforge.net/mailarchive/message.php?msg_id=28623671).

Do you have any plans on updating abyss-samtoafg (or
samtoafg) to handle gaps?

Incidentally, SSAHA2 can output alignments in other formats:
aln, cigar, gff, psl, and sugar. Perhaps it would be easier
to convert one of these other formats to afg or AMOS bank?

Thanks for your help or comments!

d f