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benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

biohack-cosmik

cactus

Official home of genome aligner based upon notion of Cactus graphs

card_nanopore_wf

WDL variant calling workflows

card_workflows

WDL workflows for the NIH CARD long-read sequencing project

docker-bayestyper

Docker container for BayesTyper

docker-bcftools-tabix

bcftools and bgzip/tabix

docker-bwa-samtools

Docker image with BWA and samtools

docker-delly

Docker container for Delly

docker-freebayes-samtools

Freebayes and samtools

docker-graphaligner

Docker container for GraphAligner

docker-graphtyper2

Docker container for GaphTyper2

docker-guppy

Docker container for guppy

docker-igv-webapp

igv-webapp + http-server to use IGV on HPC or a cloud instance

docker-liftover

Docker container for liftOver and the chain file hg19 -> GRCh38

docker-liger2liger

Docker for Liger2LiGer (rlorigro/Liger2LiGer)

docker-manta

Docker image for forked version of Manta that works with ABRA2-realigned BAMs

docker-merge-sv-vg

Container with tools to parse and merge VCFs containing SV calls from vg.

docker-pgge

Docker container to run pgge (https://github.com/pangenome/pgge)

docker-phasebook

Docker container for Phasebook: https://github.com/phasebook/phasebook

docker-repeatmasker

Docker container for RepeatMasker

docker-seqwish

Container for seqwish

docker-smoothxg

Container for smoothxg

docker-snakemake-singularity

Container to run Snakemake pipeline using singularityin its rules.

docker-svtyper

Docker container for SVTyper

docker-terra-notebook-custom

Custom Jupyter notebook with more tools

docker-terra-rstudio-custom

Custom image to use Rstudio on Terra with more packages installed

docker-ttmars

Docker container to run https://github.com/ChaissonLab/TT-Mars

docker-vg

Container with vg and a few other tools (snakemake, bcftools, awscli)

docker-vg-work

Docker container with vg and a few other tools