Illumina paired end data to use in newbler

Preparation of illumina paired end data for using in gsAssmebler

• convert the illumina .txt file to standard .fastq file with maq script fqall2std.pl --- perl fqall2std sol2std test.txt test.fastq

• convert the illumina fastq to sanger fastq --- maq sol2sanger test.fastq test1.fastq
• convert the sanger fastq to fasta and qual --- perl fqall2std.pl std2qual out.prefix test1.fastq
• convert the headers of fasta and quals for newbler so that it can recognize it as paired end --- perl replacefasta.pl test1.fasta F lib > test1.fna --- perl replacefatsa.pl test1.qual F lib > test11.qual
• rename test11.qual to test1.qual
• be sure your fna and qual files are in same folder