actually add support for native barcodes 13-24 - Githubissues

kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers

MIT License

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actually add support for native barcodes 13-24 #12

Closed kapsakcj closed 4 years ago

kapsakcj commented 4 years ago

Currently the gpu-basecalling script only checks for native barcodes 1-12 upon using ligation and yes barcoding options.

In 01_basecall-w-gpu.sh:

guppy_basecaller [more options] \
                    --barcode_kits "EXP-NBD104"

This should make guppy look for all native barcodes 1-24:

guppy_basecaller [more options] \
                    --barcode_kits "EXP-NBD104 EXP-NBD114"

according to these directions: https://community.nanoporetech.com/protocols/Guppy-protocol/v/gpb_2003_v1_revq_14dec2018/barcoding-demultiplexing

For future reference:

EXP-NBD104 = native barcodes 1-12
- https://store.nanoporetech.com/us/catalog/product/view/id/298/s/native-barcoding-expansion-1-12/category/28/
EXP-NBD114 = native barcodes 13-24
- https://store.nanoporetech.com/us/catalog/product/view/id/299/s/native-barcoding-expansion-13-24/category/28/

Should have checked before I published the v0.4.2 release 🤦