sra

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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.

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

Pipeline to fetch metadata and raw FastQ files from public databases

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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.

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

Rust-based sra-tools

Builds a PEP from SRA or GEO accessions

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

Interactive R package to quantify, analyse and visualise alternative splicing

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

A pipeline for viral identification from metagenomic samples

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

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Bioinformatics analysis of SARS-CoV-2

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

Pipeline for RNA-seq analysis