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It looks right now like bfast may be my best bet. I noticed bwa doesn't allow paired-end reads for sequences longer than ~200bp. -
Would bwa work? I need gapped alignments which bowtie cannot do, and I'd also like to get SAM-format output.Leave a comment:
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Best tool for the job (noob question)
What are the best tools for aligning a query against a target with the following characteristics? I had previously tried bowtie but only got 6% alignment when over 90% was expected:
Query file:
> Format: multisequence fasta
> Number of sequences: 180,099
> Minimum sequence length: 69 bases
> Maximum sequence length: 1,045 bases
> Average sequence length: 825 bases
> Number of Ns in file: 158,231
> Longest N stretch: 363
> Number of sequences containing N: 59,998
Target file:
> Number of sequences: 1,168
> Minimum sequence length: 1,028 bases
> Maximum sequence length: 63,086,992 bases
> Average sequence length: 843,760 bases
> Number of Ns in file: 18,289,543
> Longest N stretch: 1,185,460
> Number of sequences containing N: 771
If anyone could point me in the right direction it would be greatly appreciated. Thanks!Last edited by bre; 01-05-2010, 10:43 AM.
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