Repositories list

• informatics-website

  Public
  FAS Informatics website

  TeX

  •

  MIT License

  •22 forks•22 stars•11 issue•00 pull requests•Updated May 4, 2026May 4, 2026

• snparcher

  Public
  Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

  Python

  •

  MIT License

  •3737 forks•8989 stars•1010 issues•00 pull requests•Updated May 4, 2026May 4, 2026

• pacbio_hifi_assembly

  Public
  A snakemake workflow for assembly with HiFi

  Python

  •22 forks•44 stars•00 issues•00 pull requests•Updated May 1, 2026May 1, 2026

• specify_web

  Public
  Conversion of HUH specify_web application to git

  PHP

  •00 forks•33 stars•00 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• scRNAseqWorkflowExplorer

  Public
  Visualization tools for exploring QC metrics, clustering, marker gene and cell type annotations from multiple scRNA-seq pre-processing workflows.

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.9k3.9k forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2026Apr 27, 2026

• cactus-snakemake

  Public
  Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters

  Python

  •

  MIT License

  •22 forks•99 stars•11 issue•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• ifxvue

  Public
  Harvard FAS Informatics Vue JS components

  Vue

  •

  GNU General Public License v2.0

  •00 forks•00 stars•00 issues•1212 pull requests•Updated Apr 24, 2026Apr 24, 2026

• biotips

  Public
  The unix tips and tricks for bioinformatics workshop

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• mafutils

  Public
  Tools for MAF files

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• AllAsia-Symbiota

  Public
  The Symbiota Virtual Flora/Fauna project is an open source software project, with central goal of developing on-line tools that aid in the generation, explorati…

  JavaScript

  •

  GNU General Public License v2.0

  •107107 forks•00 stars•00 issues•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• scRNAseq-preprocessing

  Public
  Documentation of and code for analyses performed to assess the effect of different methods for cleanup and pre-processing of raw scRNAseq data on downtream anal…

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• scRNAseqClusterDownsample

  Public
  Bootstrap resampling of scRNA-seq datasets to evaluate cluster stability

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• ifxurls

  Public
  Tools for getting urls in the ifx environment

  Python

  •

  GNU General Public License v2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• specify_rapid

  Public
  Rapid data upload tool for specify. Conversion from SVN.

  JavaScript

  •00 forks•11 star•00 issues•33 pull requests•Updated Mar 27, 2026Mar 27, 2026

• short-trainings

  Public
  Material for our various standalone short trainings (a potpourri, if you will)

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 13, 2026Mar 13, 2026

• github-intro

  Public
  A hands-on introduction to git/github

  MIT License

  •1616 forks•11 star•00 issues•33 pull requests•Updated Mar 11, 2026Mar 11, 2026

• AnnotationRNAseqAssembly

  Public
  Snakemake workflow for assembling transcript models from RNA-seq reads

  Python

  •00 forks•44 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• cannon-snakemake-cfg

  Public
  Config and scripts for Snakemake's automatic partition selection on Cannon

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 4, 2026Mar 4, 2026

• bauer_static

  Public
  static page for bauer

  00 forks•00 stars•00 issues•00 pull requests•Updated Dec 18, 2025Dec 18, 2025

• snakemake-executor-plugin-cannon

  Public
  A Snakemake executor plugin for submitting jobs to the Harvard Cannon cluster

  Python

  •

  MIT License

  •5050 forks•00 stars•00 issues•00 pull requests•Updated Dec 17, 2025Dec 17, 2025

• snakemake-workshop

  Public
  Snakemake workshop

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 10, 2025Dec 10, 2025

• nextflow-workshop

  Public
  Workshop to teach how to run nextflow pipelines

  Nextflow

  •

  Other

  •00 forks•11 star•00 issues•11 pull request•Updated Dec 10, 2025Dec 10, 2025

• fiine.client

  Public
  Swagger generated client for interacting with fiine

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 9, 2025Dec 9, 2025

• ONT-basecalling-benchmark

  Public
  Snakemake pipeline to test different ONT basecalling models and protocols

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 14, 2025Nov 14, 2025

• intro-r

  Public
  The introduction to R workshop

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 27, 2025Oct 27, 2025

• python-intensive

  Public
  FAS Informatics Python Workshop

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 11, 2025Sep 11, 2025

• AnnotationBRAKER

  Public
  Workflows and code for generating and filtering genome annotations with BRAKER

  Python

  •00 forks•44 stars•00 issues•00 pull requests•Updated Aug 29, 2025Aug 29, 2025

• PhyloAcc-interface

  Public
  Front-end for PhyloAcc

  Python

  •

  GNU General Public License v3.0

  •11 fork•11 star•22 issues•00 pull requests•Updated Aug 28, 2025Aug 28, 2025

• scrub-jay-genomics

  Public
  HTML

  •

  MIT License

  •00 forks•1717 stars•44 issues•00 pull requests•Updated Aug 6, 2025Aug 6, 2025