Repository name: Illumina Assembly Maintainer: Jorge Langa - jorge.langa.arranz at gmail dot com

This repository contains tools and scritps for:

• Illumina adaptor finding (custom script)
• Read trimming (trimmomatic and seqclean)
• Transcriptome assembly (trinity)

The entire pipeline is packed into a Snakefile (a mix between of GNU make and Python3)

Requirements

• GNU Parallel (for simple parallelization)
• Seqclean and associated binaries (psx, cdbyank, cdbfasta, etc) present in the path (please test the missing libraries of each binary with ldd; I think it was libc6-dev the one missing)
• Trinity associated software (bowtie1|2, samtools, etc.)
• Snakemake (pip3 install snakemake; python3 required)

Usage

1. Create a folder called data/fastq_raw
2. Use the scripts/find_adaptors.sh script to determine the set of Illumina adaptors used. Output is on data/adaptors folder
3. Modify the Snakefile in a fashion that:
   • The SAMPLES variable contains the names of the samples to be analyzed, i.e., if your files are named sample_1.fastq.gz and sample_2.fastq.gz, then SAMPLES="sample1"
   • The ADAPTORS variable points towards the desired adaptors file in ./src/trimmomatic-0.33/adapters/file.fa
4. Type snakemake to run the pipeline