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ascat

ASCAT copy number R package

bamreport

Report on a BAM file

biomine

Bioinformatics data-mining

biotools

Scripts and pipelines for internal use

charger

Characterization of Germline variants

cnvtk

Call CNVs based on read-depth signal.

covid-19-data

An ongoing repository of data on coronavirus cases and deaths in the U.S.

crossmap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

dbassign

Assign sequences to reference genomes in a database

dotfiles

Configuration files for a fresh installation

dpviz

Visualize read depth from a GATK vcf file

galaxy-genome-diversity

Galaxy wrappers for the Genome Diversity set of tools from Bedoya-Reina et al., (2013) Galaxy tools to study genome diversity. GigaScience 2:17

graphtyper

Population-scale genotyping using pangenome graphs

hla-la

Fast HLA type inference from whole-genome data

kmertk

Tools to assist with k-mer analyses.

lastz

Program for aligning DNA sequences, a pairwise aligner.

ldtools

Analyze the patterns of linkage disequilibrium

marva

mediabuilder

Author your academic documents in markdown

millerplot

Draw linear plot to show variants.

multik

MultiK is a data-driven tool that objectively assesses the optimal number(s) of clusters based on the concept of consensus clustering via a multi-resolution perspective.

nanopore_assembly_and_polishing_assessment

Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of assembly and polishing

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

nipter

R Package for Non Invasive Prenatal Testing (NIPT) analysis

parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

qspipeline

Simple pipeline to run QuasiRecomb on fastq files

reveal.js

The HTML Presentation Framework

rna_seq_lesson

Website for "Introduction to RNA-Seq analysis, Fall 2023" at https://aakrosh.github.io/rna_seq_lesson/

scarhrd

segmentum

Segmentum a fast tool for copy number analysis of cancer genome