themariya

v0.16.1-r375, https://github.com/chhylp123/hifiasm

https://github.com/Molmed/snpseq_metadata

cDNA_Cupcake: https://github.com/Magdoll/cDNA_Cupcake

v2.4: https://github.com/Oshlack/JAFFA

v1.6, https://github.com/schneebergerlab/syri

v4.0.0rc1, https://github.com/mummer4/mummer

v1.3.0, https://github.com/ryanlayer/samplot

v0.0.8, https://github.com/dellytools/sansa

v5.2.0, https://github.com/ablab/quast

v1.0.3, https://github.com/bcgsc/longstitch

v2.2, https://github.com/marbl/canu. Includes Java and Gnuplot

v2.0.1, https://github.com/bcgsc/LINKS

v1.5.0 without CUDA, https://github.com/lbcb-sci/racon

nanofilt v2.8.0, https://github.com/wdecoster/nanofilt

flye v2.9.1-b1780, https://github.com/fenderglass/Flye

Porechop v0.2.4: https://github.com/rrwick/Porechop

pbmm2 v1.9.0: https://github.com/PacificBiosciences/pbmm2/

SQANTI3 v5.0, see: https://github.com/ConesaLab/SQANTI3

https://github.com/TomSkelly/MatchAnnot

See: https://github.com/vpc-ccg/genion

IsoSeq v3.7.0, see https://github.com/PacificBiosciences/IsoSeq

LongGF v0.1.2. See: https://github.com/WGLab/LongGF/tree/v0.1.2

A docker image containing bcftools 1.15.1. See http://www.htslib.org/

Docker container running bedtools v2.27.1

A docker image containing sambamba 0.8.2. See https://github.com/biod/sambamba

A docker image containing samtools 1.15.1. See http://www.htslib.org/

Docker image for WhatsHap: https://whatshap.readthedocs.io/en/latest/

Docker image containing Sniffles2 long-read SV caller: https://github.com/fritzsedlazeck/Sniffles