- Trimmomatic or Fastp
- BWA-MEM or Bowtie2
This guide provides detailed instructions step by step on how to set up your own HaVoC.
Install bioinformatics software
This section provides code for installing mac/unix machine.
# 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.
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 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.
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.