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dvera / albacore

Dockerfile for the Albacore basecaller from Oxford Nanopore
GNU General Public License v3.0
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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