# albacore
Dockerfile for the Albacore basecaller from Oxford Nanopore

## usage
cd into the directory containing the `reads` directory

```bash
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   |