create-reference-indices

A snakemake workflow to create reference indices and other supplementary files required for sequence analysis

Usage

Editing config file

Edit config file to point to correct reference fasta and gtf annotation file.

fa: 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh37_mapping/GRCh37.primary_assembly.genome.fa.gz'
gtf: 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh37_mapping/gencode.v31lift37.annotation.gtf.gz'

Refer to the config file for details of other configurable params

Launching the workflow

Launch using conda as follows

snakemake --use-conda

This will tell snakemake to create environments for the different tools used.