This guide provides detailed instructions step by step on how to set up your own HaVoC.
This section provides code for installing mac/unix machine.
Trimmomatic
wget
unzip Trimmomatic-0.39.zip
# set Trimmomatic instalation dir and parameters in pipeline.my.config:
TRIMM_BASE = $INSTALL_BASE/Trimmomatic-0.39
TRIMM_JAR = $TRIMM_BASE/trimmomatic-0.39.jar
TRIMM_PAR = ILLUMINACLIP:$TRIMM_BASE/adapters/TruSeq3-PE.fa:2:30:10 ..
Trimmomatic performs a variety of useful preprocessing tasks for illumina paired-end and single ended data. See the documentation of
Fastp
wget
chmod 755 fastp
cp fastp ~/bin/
# set Fastp parameters in pipeline.my.config
FASTP_PAR = -q 15 -u 40 -l 36 --detect_adapter_for_pe --cut_right ..
Fastp is a fast all-in-one read preprocessing software similar to Trimmomatic. Fastp includes automated adapter detection and polyG tail trimming. For further information refer to
BWA-MEM
BWA is a fast and accurate aligner designed to align reads and other short DNA sequences against large reference genomes. See the documentation of
Bowtie2
Samtools
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. See the documentation of
BEDtools
Lowfreq
Pangolin