albacore

Dockerfile for the Albacore basecaller from Oxford Nanopore

usage

cd into the directory containing the reads directory

docker run -v $PWD:$PWD -w $PWD -u $UID \
vera/albacore \
--recursive \
-t $(nproc) \
-i reads \
-c /opt/albacore/r94_450bps_linear.cfg \
-s output \

Available flowcell + kit combinations are:

flowcell	kit	barcoding	config file
FLO-MIN106	SQK-LSK108		r94_450bps_linear.cfg
FLO-MIN106	SQK-LSK208		r94_250bps_2d.cfg
FLO-MIN106	SQK-LWB001	included	r94_450bps_linear.cfg
FLO-MIN106	SQK-LWP001		r94_450bps_linear.cfg
FLO-MIN106	SQK-RAB201	included	r94_450bps_linear.cfg
FLO-MIN106	SQK-RAD002		r94_450bps_linear.cfg
FLO-MIN106	SQK-RAS201		r94_450bps_linear.cfg
FLO-MIN106	SQK-RBK001	included	r94_450bps_linear.cfg
FLO-MIN106	SQK-RLB001	included	r94_450bps_linear.cfg
FLO-MIN106	SQK-RLI001		r94_450bps_linear.cfg
FLO-MIN106	SQK-RNA001		r94_70bps_rna_linear.cfg
FLO-MIN106	VSK-VBK001		r94_450bps_linear.cfg