splitaake is a reasonably easy method for demultiplexing Illumina reads using either Hamming distance or Levenshtein (edit) distance sequence tags. A the moment, Hamming distance is the default, which is similar to the approach Illumina uses in their own software. splitaake differs from the Illumina software in that it can demultiplex sequence tags of many lengths, rather than just the "standard" TruSeq index length of 6 nucleotides.
splitaake is under development. This means that it may break, be a pain to get running, etc. I'll improve as I have time. Please feel free to suggest contributions/changes/additions.
splitaake is currently designed as a single-core application meaning that it does not parallelize the process of demultiplexing. After a number of tests, I've found that for most files, a single core approach is reasonably fast (and sometimes faster) than multi-core options, particularly when you wish to work with gzipped fastq files.
I'm still testing additional ways of demultiplexing data in parallel. Hopefully more on this front soon...
seqtools ("working" branch):
pip install git+git://github.com/faircloth-lab/seqtools.git@working
jellyfish (at the moment - quite fast Hamming implementation):
pip install git+git://github.com/sunlightlabs/jellyfish
generate a config file mapping indexes to filenames. This file is named map.conf, as used below:
TruSeq1:ATCACGATCT TruSeq2:CGATGTATCT TruSeq3:TTAGGCATCT TruSeq4:TGACCAATCT TruSeq5:ACAGTGATCT TruSeq6:GCCAATATCT TruSeq7:CAGATCATCT TruSeq8:ACTTGAATCT TruSeq9:GATCAGATCT TruSeq10:TAGCTTATCT TruSeq11:GGCTACATCT TruSeq12:CTTGTAATCT
python splitaake.py L007_R1.fastq.gz L007_R2.fastq.gz L007_R3.fastq.gz map.conf --section taxa
this will identify your reads and create a directory dmux containing your reads in interleaved, fastq, gzip files, like so:
dmux/ TruSeq1.fastq.gz TruSeq2.fastq.gz TruSeq3.fastq.gz ...