deconvolve
- paired-end reads from an Illumina sequencer in FASTQ format
❤️
gzipped recommended
- sample name: a-z 0-9 . _ - case insensitive
- forward: _F .F .1 _1 _R1_001 .R1_001 _R1 .R1
- reverse: _R .R .2 _2 _R2_001 .R2_001 _R2 .R2
- fastq extension: .fq .fastq case insensitive
- barcode: must be the terminal comment in the FASTQ header
The importance of doing barcode deconvolution at the FASTQ stage varies based on your goals. This table, by no means exhaustive, outlines if you should invest in it:
This workflow uses a reference-free method, QuickDeconvolution, which uses k-mers to look at "read clouds" (all reads with the same linked-read barcode) and decide which ones likely originate from different molecules. Being a reference-free method, QuickDeconvolution reads all the sequences into memory, so it can require quite a bit of RAM. More threads will increase RAM demand.
harpy deconvolve OPTIONS... INPUTS...harpy deconvolve path/to/data/*.fqRunning Options
Resulting Barcodes
After deconvolution, some barcodes may have a hyphenated suffix like -1 or -2 (e.g. A01C33B41D93-1).
This is how deconvolution methods create unique variants of barcodes to denote that identical barcodes
do not come from the same original molecules. QuickDeconvolution adds the -0 suffix to barcodes it was unable
to deconvolve.