Pipeline to fetch metadata and raw FastQ files from public databases

Package for fetching metadata and downloading data from SRA/ENA/GEO

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Interactive R package to quantify, analyse and visualise alternative splicing

GEO RNA-seq Experiments Processing Pipeline

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.

Introduction to bioinformatics command line tools on the cloud, developed by Dartmouth College

Builds a PEP from SRA or GEO accessions

Bioinformatics analysis of SARS-CoV-2

GEfetch2R - Access Single-cell/Bulk RNA-seq Data from Public Repositories and Benchmark the Subsequent Format Conversion Tools

A pipeline for viral identification from metagenomic samples

Poster for Biology of Genomes 2019 (#bog19) on recount-brain

SRA Terraform Provider

Wraps up some SRA-related utilities

Work on and around an interactive metadata table for project identification