fantauzzi

gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF

Choosing_Genomics_Tools

A course to help learners find resources and tools to help them process and interpret their genomic data

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Azimuth

Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

go-librespot

Yet another open source Spotify client, written in Go.

MACS

MACS -- Model-based Analysis of ChIP-Seq

rstudio

RStudio is an integrated development environment (IDE) for R

hisat2

Graph-based alignment (Hierarchical Graph FM index)

r-builds

an opinionated environment for compiling R

gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

Arioc

Arioc: GPU-accelerated DNA short-read alignment

falco

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

ref-gen

Human reference genome analysis sets

CHM-eval

gatk

Official code repository for GATK versions 4 and up

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Platypus

A Free and Open Source Python Library for Multiobjective Optimization

stat_rethinking_2024

stat_rethinking_2023

Statistical Rethinking Course for Jan-Mar 2023

python-fire

Python Fire is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

dsbook-part-1

Repository for Introduction to Data Science Book

Research_Technology_Bioinformatics

A Series of Tufts Research Technology Bioinformatics Workshops

spades

SPAdes Genome Assembler

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

bowtie2

A fast and sensitive gapped read aligner

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

fastx_toolkit

FASTA/FASTQ pre-processing programs