Demultiplexing (aimux)

aimux demultiplexes short-read sequencing data using a samples + barcodes annotation table. The input is a TAB-delimited file of samples and barcodes, for example (annotation.tab):

sample_id   barcode1   barcode2
sample1     ATTCGT     ACC
sample2     AGGTCC     ATT
...

Having R1, R2, I1 and I2 fastq files, aimux can be run with:

pybio aimux -r1 r1.fastq.gz -r2 r2.fastq.gz -i1 i1.fastq.gz -i2 i2.fastq.gz \
    -annotation annotation.tab \
    -barcodes barcode1:i1:RRRRRR_0_m1,barcode2:i2:RRR_0 \
    -stats aimux.stats \
    -output samples

This matches the I1 sequence against a reversed barcode1 of length 6 (RRRRRR), starting at position 0 in the I1 read (_0) and allowing 1 mismatch (_m1). At the same time, it checks the I2 sequence against barcode2, requiring a perfect match (no _m given) and again starting at position 0. Demultiplexed output is written under samples (-output), and matching statistics to aimux.stats.