Pipeline for alignment of Illumina bisulfite sequencing data and associated tools
Author: Aaron Statham (a.statham@garvan.org.au)
Execute in the directory containing the genome for aligning to as a single multifasta file with the name {Genome}.fa
To build an index for the human genome:
# Download and extract the genome
wget -O - http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz | tar -zxv
# Concatenate into a multifasta file
cat *.fa > hg19.fa
rm chr*.fa
# Build index
prepare_genome.sh hg19
Master script for aligning a lane of data. Raw data must be named in the format:
input/{Project}_R1.fastq.gz input/{Project}_R2.fastq.gz
or for a single end experiment:
input/{Project}.fastq.gz
Aligned data, methylation calls and run metrics will be put in a folder named "output".
The pipeline qsubs the following steps