accuracode's Introduction

AccuraCode

AccuraCode is a bioinfomatics analysis pipeline developed at Singleron to process AccuraCode sequencing data. This pipeline takes paired-end FASTQ files as input and generates output files which can be used for downstream data analysis.

Detailed docs can be found in manual.

Hardware/Software Requirements

minimum 32GB RAM(to run STAR aligner)
conda
git

Installation

Clone repo

git clone https://github.com/singleron-RD/AccuraCode.git

Install conda packages

cd AccuraCode
conda create -n accuracode
conda activate accuracode
conda install -y --file conda_pkgs.txt --channel conda-forge --channel bioconda --channel r --channel imperial-college-research-computing

Install accuracode

python setup.py install

Reference genome

Homo sapiens

mkdir hs_ensembl_99
cd hs_ensembl_99

wget ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz

gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh38.99.gtf.gz

conda activate accuracode
accuracode accura mkref \
 --genome_name Homo_sapiens_ensembl_99 \
 --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa \
 --gtf Homo_sapiens.GRCh38.99.gtf

Mus musculus

mkdir mmu_ensembl_99
cd mmu_ensembl_99

wget ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz

gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz 
gunzip Mus_musculus.GRCm38.99.gtf.gz

conda activate accuracode
accuracode accura mkref \
 --genome_name Mus_musculus_ensembl_99 \
 --fasta Mus_musculus.GRCm38.dna.primary_assembly.fa \
 --gtf Mus_musculus.GRCm38.99.gtf