[AMOS-help] fasta to afg

[George T. <gts...@gm...>]

Dear all,

I have sequence data from Illumina that contain sequences from two different
organisms. What I am trying to do is to map the Illumina sequences to one of
the two organisms using the AMOScmp-shortReads.
The steps that I have done so far are:

1. I convert the Illumina fastq files to fasta

2. I have the reference file as a 1con file

3. I am trying to convert the fasta file from step 1 to afg but it takes
ages for the conversion to complete (the computer is still running after 2
days but without success). The fasta file that I am trying to convert has a
size of 3.4Gb with 25,671,132 sequences.

Any suggestions?

Thanx

George








AMOScmp-shortReads data are in a fastq format. So I convert them to fasta
using

George Tsiamis, Ph.D.
Lecturer in Environmental Microbiology
Department of Environmental and Natural Resources Management
University of Ioannina
2 Seferi str., Agrinio
30100, Greece
e-mail: gts...@cc..., gts...@gm...
tel. +302641074149, fax. +302641033716