merenlab / reads-for-assemblyLinks
Simulate metagenomic short reads from one or more populations.
☆26Updated 10 months ago
Alternatives and similar repositories for reads-for-assembly
Users that are interested in reads-for-assembly are comparing it to the libraries listed below
Sorting:
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 5 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 5 years ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- Split Kmer Analysis☆65Updated 3 years ago
- Estimate metagenomic coverage and sequence diversity☆57Updated this week
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Gene-flank analysis tool☆34Updated 11 months ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- More scalable dereplication for metagenome assembled genomes☆74Updated this week
- Scalable creating/updating of metagenome profiling databases☆62Updated 5 months ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆51Updated 3 years ago
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆25Updated 2 years ago
- Recombination-free trees☆62Updated 3 months ago
- A toolbox for improving metagenome-assembled genomes.☆62Updated 4 years ago
- tools for assessing the accuracy of genome assemblies☆35Updated last year
- Automatic eukaryotic taxonomic classification☆28Updated 7 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆60Updated 2 weeks ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- ☆37Updated 3 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 3 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆59Updated 8 months ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 5 years ago