StrainEst - abundance estimation of strains
☆20Jan 17, 2020Updated 6 years ago
Alternatives and similar repositories for strainest
Users that are interested in strainest are comparing it to the libraries listed below
Sorting:
- A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).☆19Jul 10, 2018Updated 7 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 years ago
- Identifying ViRal and Circular content in metAgenomes☆14Dec 13, 2018Updated 7 years ago
- Detect contigs of complete circular genomes☆23Jun 6, 2019Updated 6 years ago
- a collection of scripts for organising bacterial genomes by species☆81Mar 18, 2022Updated 3 years ago
- A selection of short scripts for analyzing microbial genomes☆14Jun 26, 2018Updated 7 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Oct 3, 2023Updated 2 years ago
- A novel method for sequence similarity estimation☆28Mar 23, 2024Updated last year
- Phage-Host Interaction Search Tool☆29Jul 8, 2024Updated last year
- Predict prokaryotic host for phage metagenomic sequences☆55Sep 17, 2024Updated last year
- An integrated pipeline for estimating strain-level genomic variation from metagenomic data☆132Oct 6, 2023Updated 2 years ago
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome☆23Nov 25, 2025Updated 3 months ago
- strain-level analysis tools☆39Oct 21, 2024Updated last year
- Command line client and Python libraries for CosmosID API☆12Oct 28, 2025Updated 4 months ago
- ☆84Sep 13, 2023Updated 2 years ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆42Sep 3, 2024Updated last year
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Bitpacked sequence trait and implementation☆16Updated this week
- Validate and submit reads using Webin-CLI in batch.☆11Aug 3, 2023Updated 2 years ago
- Pan-genome Analysis☆12May 4, 2025Updated 10 months ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Dec 28, 2019Updated 6 years ago
- Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.☆23Nov 7, 2025Updated 3 months ago
- Python bindings for the TaxonKit library☆43Feb 2, 2026Updated last month
- Assessing the quality of prokaryotic genomes, filtering and dereplication☆11Aug 26, 2022Updated 3 years ago
- A pipeline for primary analysis of shotgun metagenomic sequencing data☆11Jun 10, 2019Updated 6 years ago
- Strain resolved metagenome simulator☆13Aug 11, 2018Updated 7 years ago
- QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture☆12Sep 22, 2022Updated 3 years ago
- SpacePHARER CRISPR Spacer Phage-Host pAiRs findER☆44May 8, 2024Updated last year
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- Library of sketching functions used by PopPUNK☆31Mar 31, 2025Updated 11 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆54Jul 3, 2024Updated last year
- frame-shift correction for long-read (meta)genomics☆33Dec 11, 2023Updated 2 years ago
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆25Feb 25, 2023Updated 3 years ago
- ☆23May 8, 2023Updated 2 years ago
- A tool to detect acquired AMR genes directly from long read sequencing data.☆20Jan 31, 2026Updated last month
- KBase distribution module for RASTtk.☆13Sep 14, 2020Updated 5 years ago
- The MG-RAST Backend -- the API server☆46Apr 27, 2023Updated 2 years ago
- ☆12Feb 22, 2022Updated 4 years ago