Bowtie with gaps

[jjk]

Searched almost all the day and only found 1 candidate that could match bowite a little bit. Im trying to find a short sequence aligner (illumina data set in fasta format) that allows gaps up to a maximum of 5 with or without mismatches. Bowtie only handles a few mismatches and no gaps, i found genomemapper but the output file is not .sam and i only know tablet for visualisation.

Thus my question is does someone knows an easy to handle short sequence aligner to a reference sequence that allows gaps/mismatches and export into a .sam format?

thanks!

[lh3]

novoalign, bwa, bfast.

[jjk]

Tried bwa, but it gives an:

BWTIncConstruct() : Not enough memory allocated!

probably due to the fact that i ran it on my laptop with only 2gb in there i think. But thanks for the fast reply ill try the other programs as well!

Just gave a ran with novocraft... so far it looks very good i only stumble on 1 problem saving the output file...

# Read Sequences: 156
# Aligned: 156
# Unique Alignment: 0
# Gapped Alignment: 0
# Quality Filter: 0
# Homopolymer Filter: 0
# Elapsed Time: 2,054s
# Done.

i ran a very short example:

./novoalign -o output.sam -f inputtest.fa -d index

but no output file has been found. what am i doing wrong?