In­stall­a­tion

In­stall­a­tion

Sys­tem re­quire­ments

Bioinformatics software

  1. Trimmomatic or Fastp
  2. BWA-MEM or Bowtie2
  3. SAMBAMBA/Samtools
  4. BEDtools
  5. Lowfreq
  6. BCFtools/Samtools
  7. Pangolin

In­stall­a­tion

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.

Trimmomatic

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomat...
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