sra
There are 58 repositories under sra topic.
saketkc/pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
wwood/kingfisher-download
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
vanheeringen-lab/seq2science
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.
nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
BioOmics/iSeq
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
louiejtaylor/grabseqs
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
pepkit/geofetch
Builds a PEP from SRA or GEO accessions
nuno-agostinho/psichomics
Interactive R package to quantify, analyse and visualise alternative splicing
showteeth/scfetch
Access and Format Single-cell RNA-seq Datasets from Public Resources
CDCgov/seqsender
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
CDCgov/tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
NCBI-Hackathons/ViruSpy
A pipeline for viral identification from metagenomic samples
linsalrob/partie
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.
uc-bd2k/GREP2
GEO RNA-seq Experiments Processing Pipeline
davetang/sars_cov_2
Bioinformatics analysis of SARS-CoV-2
rohitsuratekar/CardioPipeLine
Pipeline for RNA-seq analysis
NIGMS/Fundamentals-of-Bioinformatics
Introduction to bioinformatics command line tools on the cloud, developed by Dartmouth College
mbernste/hypothesis-driven-SRA-queries
Find structured-datasets from within the Sequence Read Archive
NCBI-Hackathons/MetadataTable
Work on and around an interactive metadata table for project identification
lucasmenendez/gopsi
Simple Private Set Intersection implemented in pure Go.
pmenzel/biq
Tool for indexing and querying back-splice junctions of circular RNAs (circRNAs) in RNA-Seq datasets
aofarrel/SRANWRP
Wraps up some SRA-related utilities
BeyondTrust/terraform-provider-sra
SRA Terraform Provider
quantori/FastqHeat
Python wrapper created to help download metagenomic data from SRA or ENA databases
arcones/sra-collector
Collect NIH NCBI SRA metadata of several GEO studies in one search
bcgsc/rsempipeline
A pipeline for running rsem analysis on thousands of samples
FOI-Bioinformatics/metaquest
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.
gavieira/mitofree
Automated mitochondrial genome assembly using SRA public data
Imamachi-n/AutoNGS
Automatic NGS data analysis from SRA download to the quantification of RNAs.
mr-eyes/sra_size_plot
Up-to-date SRA growth size visualization
UnseenBio/sra-demo-benchmark
A demo workflow showing download, extraction, and compression of sequences from SRA.
zkCohort/sra-wasm
An SRA library through which web assembly is provided as an interface to generate SRA public and private keys client side
snipe-bio/snipe
Blazingly fast SRA-scale sequence analysis & QC
applicativesystem/sra-explorer
explore sra databases and sequence retrieval
asadprodhan/A-Guide-to-Automatically-Downloading-NCBI-SRA-Reads
A Guide to Automatically Downloading NCBI SRA Reads
Fi-Santos/sra2fastq
Bash script for downloading, converting, and analyzing SRA files to FASTQ format with quality control using FASTQC.