Alevin-fry

Alevin-fry is a suite of tools for the rapid, accurate, and processing of single-cell and single-nucleus sequencing data. It expects a RAD file from either salmon alevin or piscem. It takes that file and a permit list based on the chemistry used to do the sequencing to scan the barcodes encountered in the data. It is important to note that it does not support RAD files generated with a decoy-aware index. As such make sure your indices for the RAD files do not include decoy sequences.

After running either salmon alevin or piscem you scan the barcodes with the following:

alevin-fry generate-permit-list --input RADFILE --expected-ori fw --output-dir OUTDIR --unfiltered-pl PERMIT.txt

Then after generating the barcode mapping you collate the original RAD file.

alevin-fry collate -i OUTDIR -r RADFILE -t THREAD_COUNT

Finally you quantify:

alevin-fry quant -i OUTDIR -m TG_MAP -t THREAD_COUNT -r cr-like -o OUTDIR

To learn more about this software please see their official documentation for more details.

Parallel Capabilities: Multithreading.