Aligning Helicos Genome Analyser Reads

Novoalign is well suited to aligning Helicos Genome Analyzer reads. We have run some tests on reads from SRA009216 and suggest following parameters.

1. The SRA009216 fastq files had low Phred quality of 15 for all bases. We suggest either converting the fastq file to fasta or increasing base qualities to 30.

2. The Heliscope seems to produce a fairly high level of insert/delete sequencing errors. To allow for these the gap penalties need to be reduced. We suggest using -g0 -x20 as this is the lowest that Novoalign will currently accept. We will release an update shortly that allows gap penalties to be set even lower.