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.
☆48Updated 4 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 last month
- Split Kmer Analysis☆66Updated 3 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆60Updated 2 weeks ago
- ☆37Updated 3 years ago
- Recombination-free trees☆62Updated 3 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 4 years ago
- Predict plasmids from uncorrected long read data☆41Updated last month
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 5 years ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- Graph-based assembly phasing☆90Updated 2 weeks ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆75Updated 2 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆103Updated 3 weeks ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Gene-flank analysis tool☆34Updated 11 months ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆39Updated last week
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆48Updated 2 weeks ago
- Bifrost graph gene caller.☆96Updated 2 months ago
- Surveillance of pathogens using population genomics and sequencing☆52Updated 3 weeks ago
- Intra-species bacterial contamination detection☆25Updated 10 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆100Updated this week
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- A toolkit for prokaryotic comparative genomics☆51Updated last month
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 3 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- tools for assessing the accuracy of genome assemblies☆35Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆32Updated last year