Issues

• check-corrupt exits 0 on corrupt runs since 3.3.0 and reports "All accessions are good!" for inputs it could not open

  ncbi/sra-tools#1202 · Filter by author Santoshkumarpuppala opened on Sep 27, 2026

• prefetch/srapath "no data (404)" for all runs in approved dbGaP cart (phs000951, project #43272)

  ncbi/sra-tools#1200 · Filter by author Neos1124 opened on Sep 4, 2026
  1

• cmake acting weird

  ncbi/sra-tools#1182 · Filter by author rubyFeedback opened on Jun 18, 2026

• fasterq-dump incomplete download

  ncbi/sra-tools#1154 · Filter by author ManuelBradicic42 opened on Feb 27, 2026

• Compilation error due to missing file

  ncbi/sra-tools#1122 · Filter by author rennigm opened on Dec 4, 2025
  3

• Best practices for batch processing SRA accessions on an HPC cluster

  ncbi/sra-tools#1113 · Filter by author Tushar-bioinfo opened on Nov 1, 2025

• fasterq-dump error code 3 associated with directory name

  ncbi/sra-tools#1110 · Filter by author NateyJay opened on Oct 22, 2025

• Does latf-load not support single-cell RNA-seq data, including index files?

  ncbi/sra-tools#1048 · Filter by author chunryongoh opened on May 12, 2025
  2

• Feature suggestion: option in fasterq-dump to output the FASTQ files already gzipped

  ncbi/sra-tools#956 · Filter by author fantauzzi opened on Aug 14, 2024
  1

• vdb-config: use AWS IAM role instead of credentials file

  ncbi/sra-tools#945 · Filter by author peter-sandor-1992 opened on Jul 4, 2024
  1

• vdb-config

  ncbi/sra-tools#936 · Filter by author anjilsri opened on May 8, 2024
  4

• consider adding a flake.nix

  ncbi/sra-tools#854 · Filter by author MatrixManAtYrService opened on Sep 30, 2023

• default parameter values tinhelp output for fasterq-dump

  ncbi/sra-tools#840 · Filter by author bwlang opened on Aug 17, 2023
  1

• Feature request: increase speed of C++ API for streaming reads from alignment-based SRA records

  ncbi/sra-tools#794 · Filter by author jgans opened on Mar 21, 2023

• fasterq-dump "--only-aligned" and "--only-unaligned" ignored when combined with "--fasta"

  ncbi/sra-tools#793 · Filter by author jgans opened on Mar 21, 2023

• fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds

  ncbi/sra-tools#732 · Filter by author mpuzio opened on Nov 6, 2022
  2

• prefetch errors out if number of files is greater than 516

  ncbi/sra-tools#722 · Filter by author angadkalra opened on Oct 3, 2022

• Fetch Max and Min read length from fastq

  ncbi/sra-tools#571 · Filter by author xexpanderx opened on Jan 6, 2022
  2

• documentation difficult for the colorblind

  ncbi/sra-tools#563 · Filter by author dpschreiner opened on Dec 15, 2021
  3

  

• Writing fasterq-dump output as a streamable not currently possible

  ncbi/sra-tools#508 · Filter by author wwood opened on May 16, 2021
  3

• sra-stat is incredibly slow for certain files

  ncbi/sra-tools#188 · Filter by author Miserlou opened on Mar 22, 2019

• Issue to collect native SRA format tools

  ncbi/sra-tools#173 · Filter by author seandavi opened on Jan 18, 2019
  2

• Sra-pileup region list issues

  ncbi/sra-tools#86 · Filter by author SichongP opened on Jun 19, 2017

• sam-dump does not add .SPOT_GROUP to QNAME for unaligned reads

  ncbi/sra-tools#49 · Filter by author buddej opened on Dec 21, 2016