Technical helpsheet
To carry on the practical exercises, you may need the following software and packages:
- Linux
- A web explorer
- java 1.8 or later https://www.oracle.com/java/technologies/downloads/
- R https://www.r-project.org/
- R packages: GenomicRanges, IRanges, argparser, tidyverse, stringdist, testthat, stringr, StructuralVariantAnnotation, rtracklayer
- alleleCount https://github.com/cancerit/alleleCount
- ASCAT https://github.com/VanLoo-lab/ascat
- ASCAT.sc https://github.com/VanLoo-lab/ASCAT.sc
- assembly-stats https://github.com/sanger-pathogens/assembly-stats
- BamToCov https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
- bbmap http://qualimap.bioinfo.cipf.es/
- bbmap https://sourceforge.net/projects/bbmap/
- BBTools: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
- Bcftools https://samtools.github.io/bcftools/bcftools.html
- Bedtools https://github.com/arq5x/bedtools2
- Breakdancer https://github.com/genome/breakdancer
- bwa http://bio-bwa.sourceforge.net/
- canu https://canu.readthedocs.io/en/latest/
- Circos https://circos.ca/software/installation/
- CTCallR https://github.com/galder-max
- Fastp: https://github.com/OpenGene/fastp
- FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- freebayes https://github.com/ekg/freebayes
- GATK https://software.broadinstitute.org/gatk/
- GFAtools https://github.com/lh3/gfatools
- GRIDSS2 https://github.com/PapenfussLab/gridss
- git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
- IGV http://software.broadinstitute.org/software/igv/, https://www.igv.org/
- LUMPY https://github.com/arq5x/lumpy-sv
- Minigraph https://github.com/lh3/minigraph
- Minimap2 https://github.com/lh3/minimap2
- mosdepth https://github.com/brentp/mosdepth
- Multiqc https://multiqc.info/
- Nextflow: https://www.nextflow.io/
- NGMLR https://github.com/philres/ngmlr
- ODGI https://odgi.readthedocs.io/en/latest/rst/installation.html
- picard https://broadinstitute.github.io/picard/
- qualimap http://qualimap.conesalab.org/
- QUAST https://github.com/ablab/quast
- sarek: https://nf-co.re/sarek/3.4.2/
- samtools http://www.htslib.org/
- slurm: https://slurm.schedmd.com/documentation.html
- ssh / ssh-keygen: https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent
- Sniffles https://github.com/fritzsedlazeck/Sniffles/wiki
- SOAPec https://omictools.com/soapec-tool
- STAR https://github.com/alexdobin/STAR
- Tablet https://ics.hutton.ac.uk/tablet/
- Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
- util-linux https://github.com/util-linux/util-linux
- vcftools https://vcftools.github.io/examples.html
- VEP variant effect predictor 112 https://www.ensembl.org/info/docs/tools/vep/script/index.html
- vg https://github.com/vgteam/vg
- wtdbg2 https://github.com/ruanjue/wtdbg2