Illumina trimming pipeline

This trims libraries from Illumina sequencing.

• Features
  • Uses snakemake for parallelization and resource management.
  • Library names are automatically determined just by specifying directories.
  • Options to specify trimming with TruSeq2 or Nextera Adapters.
  • Options to trim Dovetail Chicago and HiC data. The junction sequence is user-specified.
  • Generates a report of trimming efficiency and linker content sequence.

Requirements

• This pipeline requires
  • Snakemake (for python 3)
  • bbmerge
  • trimmomatic
  • gcc

Instructions

There is an example called directories.yaml(example). Rename your actual file to directories.yaml. Run snakemake --cores <num_cores> -p -r in the directory with the directories.yaml, bin/, and Snakemake files.