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 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39…
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 Trimmomatic for further information.
Fastp
wget http://opengene.org/fastp/fastp
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 Fastp documentation.
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 Burrow-Wheeler Aligner for installation and use.
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 Samtools for installation and use.
BEDtools
Lowfreq
Pangolin