Additional Software

Additional Bioinformatics Software Installed

Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic
Qualimap: http://qualimap.conesalab.org
HISAT2: https://daehwankimlab.github.io/hisat2
StringTie: https://ccb.jhu.edu/software/stringtie
STAR: https://github.com/alexdobin/STAR
Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
RSEM: https://github.com/deweylab/RSEM
DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Salmon: https://salmon.readthedocs.io/en/latest/salmon.html
edgeR: https://bioconductor.org/packages/release/bioc/html/edgeR.html
Bedtools: https://bedtools.readthedocs.io/en/latest/index.html
VCFtools: https://vcftools.github.io
Picard: https://broadinstitute.github.io/picard/
Canu: https://canu.readthedocs.io/en/latest
BCFtools: https://samtools.github.io/bcftools/bcftools

And much more!

Genomics Software

Verkko Telomere-to-telomere assemblies: https://github.com/marbl/verkko
FALCON & FALCON-unzip - PacBio: https://pb-falcon.readthedocs.io/en/latest/about.html
MaSuRCA - Illumina, PacBio, Nanopore: https://github.com/alekseyzimin/masurca
SPAdes - Illumina, PacBio, Nanopore: https://github.com/ablab/spades
Hinge - PacBio, Nanopore: https://github.com/HingeAssembler/HINGE
Abyss - Illumina: https://github.com/bcgsc/abyss
Shasta - Nanopore: https://github.com/paoloshasta/shasta