harvardinformatics

GenomeAnnotation

Best practices and workflow for genome annotation

snpArcher

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

TranscriptomeAssemblyTools

A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.

degenotate

AnnotationTOGA

Guidelines for running TOGA and scripts for processing outputs

scrub-jay-genomics

website

Website markdown files

ifxdjango

Django project template for ifx Django REST / VueJS / Vuetify applications

specify_web

Conversion of HUH specify_web application to git

BulkRNAseq2Counts

A Snakemake workflow for generating expression count tables from either locally stored fastq files or NCBI-SRA accessions for bulk RNA-seq

pacbio_hifi_assembly

A snakemake workflow for assembly with HiFi

AnnotationBRAKER

Workflows and code for generating and filtering genome annotations with BRAKER

specify_rapid

Rapid data upload tool for specify. Conversion from SVN.

djvocab

Vocabulary table for Django

ifxurls

Tools for getting urls in the ifx environment

ifxvue

Harvard FAS Informatics Vue JS components

AllAsia-Symbiota

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, exploration and management of biodiversity data (collection specimens, observations, images, checklist, keys, etc.). See also: http://bdj.pensoft.net/articles.php?id=1114 and http://symbiota.org/

AnnotationRNAseqAssembly

Snakemake workflow for assembling transcript models from RNA-seq reads

bioconda-recipes

Conda recipes for the bioconda channel.

bird-dfe

cnstoolsearch

django-cas-server

A Django Central Authentication Service server implementing the CAS Protocol 3.0 Specification

EndoriftiaTranscriptomics

Code used in data analysis for Mitchell et al. 2024, a forthcoming paper on transcriptomic responses to environmental variation in *Candidatus Endoriftia persephone*, a bacterial symbiont of the deep sea tubeworm *Riftia pachyptila*.

github-intro

A hands-on introduction to git/github

informatics-website

FAS Informatics website

IP4CI

IP4CI: an interpretable pathway-based computational method for cross-species cell-type identification from single cell data

Mapping-simulations

Read mapping simulations while varying divergence levels

mop

Simple tool for capturing alignment regions with sufficient quality for genotyping.

parse-pileup

PEA