linsalrob / partieLinks
PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.
☆24Updated 2 years ago
Alternatives and similar repositories for partie
Users that are interested in partie are comparing it to the libraries listed below
Sorting:
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- Extract lineage CSVs from NCBI for use with sourmash lca.☆29Updated 2 years ago
- Strain Prediction and Analysis with Representative SEquence☆19Updated 11 months ago
- Get microbial sequence data easier and faster☆28Updated 6 years ago
- Protein Alignment and Detection Interface☆60Updated last year
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆25Updated last year
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated last month
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Updated 4 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 8 years ago
- Simulate metagenomic short reads from one or more populations.☆26Updated 9 months ago
- Utility program for extracting sequences from a fasta/fastq file☆35Updated 10 months ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Updated 4 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- Locus and lineage tests for bacterial GWAS☆29Updated 8 years ago
- Assign taxonomic ranks based on evolutionary divergence.☆23Updated 3 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- MAG Circularization Method☆32Updated 2 weeks ago
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆47Updated 4 months ago
- Antibiotic resistance predictions in minutes on a laptop☆50Updated 6 years ago
- StrainEst - abundance estimation of strains☆20Updated 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
- Scalable creating/updating of metagenome profiling databases☆62Updated 4 months ago
- Strain Resolution ON Graphs☆48Updated 2 years ago
- Detect contigs of complete circular genomes☆23Updated 6 years ago