Converting raw signals (i.e. Squiggle) to FAST5

The officially supported tool for converting squiggle signals to FAST5 reads is "albacore". Use the following command to perform this conversion:

qsub -j yes -t 1-<(#batch_dir)+1> basecall.sh <input_dir> <output_dir> <cfg_name>

For configs (i.e. <cfg_name>) the following options can be used:

• Ligation Sequencing Kit 1D (SQK-LSK108, R9.4):

  • FLO-MIN106_LSK108_linear.cfg
  • FLO-MIN107_LSK108_linear.cfg (r95_450bps_linear.cfg)

• Ligation Sequencing Kit 2D (SQK-LSK208, R9.4):

  • FLO-MIN106_LSK208_linear.cfg
  • FLO-MIN106_LSK208_tc.cfg
  • FLO-MIN106_LSK208_2d.cfg

• Rapid Sequencing Kit (SQK-RAD001):

  • FLO-MIN106_RAD001_linear.cfg

• Rapid Sequencing Kit (SQK-RAD002):

  • FLO-MIN106_RAD002_linear.cfg