Hello everyone,
I'm analysing Solexa reads from a bacterial genome currently unavailable. As first step, of course, I'm trying to assemble the reads, and my pipeline includes AMOScmp as an important step in the assemblage. However, my Solexa library has more than 11 millions reads, with 36 bp each, and I just can't compile the AFG file for insufficient memory. I tried in many computers, and the best I reached was ~9 millions reads in a tmp file (using a machine with 16Gb in RAM), but I just can't get the work complete.
I have the same library in a variety of other formats, such as PRB (the original file), fastQ (Solexa and Sanger/Standard), Fasta/Qual, and even the WGS' FRG format. Unless the last one is pretty similar to AFG, I can't make toAmos convert FRG to AFG.
Does anyone know how to convert FRG (wgs-assembler) to AFG (AMOS) in a memory efficient way?, or otherwise, does anyone know how to merge two AFG files into a single one?
I tried to make a script for AFG merging, but I'm still having some issues with the format definition, such as "What does FRG's eid means?" or "How must I order the RED's frg?".
Thanks in advance!
I'm analysing Solexa reads from a bacterial genome currently unavailable. As first step, of course, I'm trying to assemble the reads, and my pipeline includes AMOScmp as an important step in the assemblage. However, my Solexa library has more than 11 millions reads, with 36 bp each, and I just can't compile the AFG file for insufficient memory. I tried in many computers, and the best I reached was ~9 millions reads in a tmp file (using a machine with 16Gb in RAM), but I just can't get the work complete.
I have the same library in a variety of other formats, such as PRB (the original file), fastQ (Solexa and Sanger/Standard), Fasta/Qual, and even the WGS' FRG format. Unless the last one is pretty similar to AFG, I can't make toAmos convert FRG to AFG.
Does anyone know how to convert FRG (wgs-assembler) to AFG (AMOS) in a memory efficient way?, or otherwise, does anyone know how to merge two AFG files into a single one?
I tried to make a script for AFG merging, but I'm still having some issues with the format definition, such as "What does FRG's eid means?" or "How must I order the RED's frg?".
Thanks in advance!
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