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bammotifsearcher

Find reads in a bam file that contain a given sequence (can contain degenerate bases)

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

bioconda-recipes

Conda recipes for the bioconda channel.

bsub_jupyter

Connect to a LSF main node directly or trough a ssh jump node, launch a jupyter notebook via bsub and open automatically a tunnel. The name of the connection can be used to reestablish the connection later or to terminate it.

bug-free-disco

chip-seq-pipeline2

chip_tutorial

clinder

conda-wdls

WDLs and conda environments for running genomic analyses on a HPC using conda (e.g. instead of docker)

crispratac

crispresso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

cutadapt

Cutadapt removes adapter sequences from sequencing reads

dockstore-tool-bamstats

A repo for the BAMStats command, used as the tutorial for Dockstore

gem

Genome Editing Metadata API

getclinvar

guidefinder

insertion_checker

mekit

methylation-workflow

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

pem-q

a pipeline to process data of PEM-seq or data similar, which is more comprehensive than superQ

shinydemo

simple_python_package_setuptools

Simple python package to demonstrate package imports with setuptools

simulateindels

strelka

Strelka2 germline and somatic small variant caller

suffix-tree

implementation of how to construct suffix tree

test_project