Mapping short reads (23 b) to large catalog of short (20 b) sequences
I have a library of 50,000 short sequences (20 bases each). I also have a fastq file from Illumina with short reads (23 bases each). I need to map the sequenced reads (first 20 bases) to the catalog, allowing for at most 1 mismatch and no indels. Could anyone point me to a suitable aligner? If you could also give me some advice on what parameters of that aligner would be suitable given this problem, that would be awesome!
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Bowtie has an explicit option to control for mismatches (-n). You may check out the manual.