Does anyone have experience with AMOS? I have used different assemblers, and usually the input file format is fastq. I am trying to figure out how to use AMOScmp to do a template-guided assembly, and I am not sure if I understand it correctly:
TGT - The genome reads to map in AMOS message format REF - The reference genome sequence in FASTA format
how would I get my usual fastq file inputs into AMOS message format (which I assume is afg?), especially considering that this is supposed to be a file format for assembly data??? if my data is already assembled, why do i need to run another assembly?? Does it mean i have to run AMOS (de novo) first, then use that output in AMOScmp? That is not what I am trying to do! (And i have tried MIRA, but it is too memory intensive apparently).
also the reference file description says fasta, but the how-to text says it's .1con. is this just a matter of changing the file name?or would AMOScmp read a reference file with fasta extension as well?
And I have checked http://sourceforge.net/apps/mediawiki/amos/index.php?title=File_conversion_utilities but being so ignorant in soo many little steps in between these are not helpful to me either. I need AMOS for Dummies, sorry about so many questions. I will be happy for ANY eplanations at all.
I would also encourage you to check out ARC. It is very simple to use and has given me great reference based assemblies.
https://github.com/ibest/ARC