An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
☆58Jul 24, 2025Updated last year
Alternatives and similar repositories for sra-human-scrubber
Users that are interested in sra-human-scrubber are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 4 months ago
- Influenza genome analysis Nextflow workflow☆28Jun 3, 2026Updated 4 months ago
- In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies☆10Aug 6, 2024Updated 2 years ago
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆123Updated this week
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 4 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Bacterial surveillance pipeline.☆30Sep 30, 2026Updated 3 weeks ago
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆19Aug 28, 2026Updated 2 months ago
- Reference-based consensus creation☆61Updated this week
- TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read…☆84Updated this week
- Pipeline for creating comprehensive viral reference sets.☆12Sep 17, 2026Updated last month
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated last year
- Split Kmer Analysis☆68May 26, 2022Updated 4 years ago
- ☆39Oct 22, 2026Updated last week
- Fast viral consensus genome reconstruction☆27Sep 16, 2026Updated last month
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- A tool for managing your pores☆10Jul 22, 2026Updated 3 months ago
- A database for signatures of public genomic sources☆18Jul 18, 2026Updated 3 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆22Oct 8, 2025Updated last year
- µbinfie blog☆19Jul 21, 2025Updated last year
- Precise host read removal☆134Apr 13, 2026Updated 6 months ago
- Intra-species bacterial contamination detection☆26Jul 10, 2026Updated 3 months ago
- Use tbl2asn forever by pretending that it's still 2019☆12Jan 24, 2020Updated 6 years ago
- Evaluating Nanopore-based bacterial variant calling☆23Oct 7, 2026Updated 3 weeks ago
- ☆17May 22, 2023Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Comprehensive resistance detection from WGS data☆22Sep 4, 2026Updated last month
- viral-ngs: complete pipelines☆75Oct 16, 2026Updated last week
- UPHL's Reference Free Pipeline☆29Oct 9, 2026Updated 2 weeks ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Dec 2, 2024Updated last year
- Benchmark datasets for WGS analysis☆40Aug 4, 2019Updated 7 years ago
- 🍗⭐ In silico Legionella pneumophila Sequence Based Typing☆13Feb 8, 2026Updated 8 months ago
- ☆13May 29, 2026Updated 5 months ago
- Systematic ProtEin AnnotatoR☆19Sep 20, 2025Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆33Oct 5, 2026Updated 3 weeks ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- Recombination-free trees☆75Jul 24, 2026Updated 3 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆103Oct 2, 2026Updated 3 weeks ago
- A repo with just adapter sequences☆14Jul 7, 2025Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆35Jul 27, 2026Updated 3 months ago
- Nextflow version of SNVPhyl☆12Oct 24, 2024Updated 2 years ago
- Rapid determination of appropriate reference genomes.☆103Jan 22, 2025Updated last year