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Tools and scripts from the Arkin Lab at UC Berkeley
Instead of outputting read names as their barcodes, skip right to naming them by sample from the provided plate layout
It would be nice if reads that were <100nt after merging could be filtered. Likewise for reads that are too long, e.g. 600nt in a 600 cycle Illumina run.
Raise --maxaccepts to a high number, lower --maxhits to 1. Report single best hit while searching entire (small) database
Split the file into multiple parts and run them separately
Add table output to merge_demultiplex, barcodes vs. number of reads
Each function should be callable on its own without referencing the options global variable. This will facilitate unit tests later on.
In merge_demultiplex.py
it is possible that a read matches barcodes in barcodes.txt that have no corresponding samples in plate_layout.py (which are there due to contamination or error). In these cases, an error is thrown. Instead, it would be preferable if these were ignored.
Make sure read length distribution matches that which is expected based on differences in barcode lengths with phasing.
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