From: d f <df6...@gm...> - 2012-09-05 18:46:20
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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 |