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

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.

一份通俗易懂的搜索、推荐、广告算法教程，同时不缺乏趣味和深度

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

Builds a PEP from SRA or GEO accessions

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

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

Bioinformatics analysis of SARS-CoV-2

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

Pipeline for RNA-seq analysis

Find structured-datasets from within the Sequence Read Archive

Work on and around an interactive metadata table for project identification

Simple Private Set Intersection implemented in pure Go.

Tool for indexing and querying back-splice junctions of circular RNAs (circRNAs) in RNA-Seq datasets

Python wrapper created to help download metagenomic data from SRA or ENA databases

Wraps up some SRA-related utilities

SRA Terraform Provider

This repository saves Train/Test datasets used for training of ESKAPEE classification work and classification results publicly available at: https://www.techrxiv.org/doi/full/10.36227/techrxiv.21675053.v5

A pipeline for running rsem analysis on thousands of samples

MetaQuest is a robust and user-friendly command-line toolkit designed to simplify and streamline the analysis of metagenomic data. From summarizing the presence of specific genomes to visualizing complex datasets, MetaQuest offers an array of tools to help researchers uncover insights from their metagenomic datasets.

A Bash script for downloading sequencing data from the NCBI SRA database.

An SRA library through which web assembly is provided as an interface to generate SRA public and private keys client side