ncbi / sra-human-scrubberLinks
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.
☆50Updated 6 months ago
Alternatives and similar repositories for sra-human-scrubber
Users that are interested in sra-human-scrubber are comparing it to the libraries listed below
Sorting:
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Updated 3 months ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆103Updated 3 weeks ago
- Split Kmer Analysis☆67Updated 3 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Updated 5 years ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated 2 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- Graph-based assembly phasing☆90Updated 2 months ago
- Recombination-free trees☆63Updated 4 months ago
- Bifrost graph gene caller.☆98Updated last week
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Updated 3 weeks ago
- Gene-flank analysis tool☆36Updated last year
- A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads☆67Updated 4 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆61Updated this week
- A toolkit for prokaryotic comparative genomics☆51Updated 3 months ago
- ☆37Updated 3 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 4 years ago
- Surveillance of pathogens using population genomics and sequencing☆52Updated 2 weeks ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Split k-mer analysis – version 2☆103Updated 2 weeks ago
- Identify phage regions in bacterial genomes for masking purposes☆33Updated 6 years ago
- A tool for removing redundant genomes from a set of assemblies☆78Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- tools for assessing the accuracy of genome assemblies☆35Updated last year
- Scalable creating/updating of metagenome profiling databases☆63Updated 7 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Updated 2 years ago
- Order and orientation of complete bacterial genomes☆29Updated 6 months ago