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.

Pipeline to fetch metadata and raw FastQ files from public databases

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

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

Builds a PEP from SRA or GEO accessions

Interactive R package to quantify, analyse and visualise alternative splicing

Access and Format Single-cell RNA-seq Datasets from Public Resources

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

A pipeline for viral identification from metagenomic samples

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

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.

GEO RNA-seq Experiments Processing Pipeline

Bioinformatics analysis of SARS-CoV-2

Pipeline for RNA-seq analysis

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

Work on and around an interactive metadata table for project identification

Find structured-datasets from within the Sequence Read Archive

Simple Private Set Intersection implemented in pure Go.