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align

Performs global and local sequence alignment.

bamsurgeon

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

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

bioconda-recipes

Conda recipes for the bioconda channel.

dep

misc dependency repo

discord-retro

Find non-reference TE insertions from discordant read pair mappings

edots

Expression Divergence Over Time Series

exonerate

A generic tool for sequence alignment

gripper

Find non-reference processed pseudogene insertions from discordant read pair mappings

gripper2

Detect gene retrocopy insertion polymorphisms (GRIPs) from short-read paired-end WGS data

iap-replication

l1seq

l1seq.old

Scripts for analyzing "L1-seq" data generated by targeted L1-specific sequencing (Ewing and Kazazian 2010, doi:10.1101/gr.106419.110)

methylartist

Tools for plotting methylation data in various ways

methylartist-tests

Test data and examples for methylartist

nanorama

Real-time overview of nanopore targeted sequencing

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

te-nanopore-tools

tools for plotting and parsing methylation aimed at TEs

tebreak

Find and characterise transposable element insertions

tldr

Identify and annotate TE-mediated insertions in long-read sequence data

vcfcomparator

Tool for comparing mutation calls in VCF format