Pipeline to generate NGS reads from a phylogeny
☆39Sep 13, 2022Updated 3 years ago
Alternatives and similar repositories for TreeToReads
Users that are interested in TreeToReads are comparing it to the libraries listed below
Sorting:
- (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join☆11Apr 29, 2021Updated 4 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated last week
- in silico plasmid extraction☆13Sep 18, 2017Updated 8 years ago
- (Obsolete) NCBI Prokaryotic Genome Annotation Pipeline. New site:☆16Sep 7, 2018Updated 7 years ago
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- SaffronTree: Reference free rapid phylogenetic tree construction from raw read data☆25Jun 11, 2020Updated 5 years ago
- A simple pipeline for bacterial assembly and quality control☆16Feb 17, 2026Updated last week
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆14Feb 19, 2026Updated last week
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- REcombination BARcode detector.☆16Apr 2, 2024Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆46Sep 3, 2020Updated 5 years ago
- The MLST pipeline developed by the PathOGiST research group☆36Nov 29, 2023Updated 2 years ago
- Classify sequencing reads using MinHash.☆48Apr 6, 2020Updated 5 years ago
- kaamer - protein identification based on amino acid kmers☆12Mar 7, 2023Updated 2 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- tools for assessing the accuracy of genome assemblies☆35Apr 16, 2024Updated last year
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Aug 26, 2024Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- A tool for removing redundant genomes from a set of assemblies☆78Sep 10, 2025Updated 5 months ago
- Pipeline for Evaluating Prokaryotic References☆11Sep 16, 2016Updated 9 years ago
- "Reads to report" for public health and clinical microbiology☆143Dec 9, 2025Updated 2 months ago
- annotation pipeline for microbial genomes and metagenomes☆18Feb 23, 2018Updated 8 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- Follow up to Grace Blackwell's 661k dataset, for 2023☆135Feb 20, 2026Updated last week
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆27Jul 21, 2025Updated 7 months ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20Oct 4, 2024Updated last year
- Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes☆31Jun 16, 2024Updated last year
- ☆11Dec 24, 2024Updated last year
- Salmonella serotyping from genome sequencing data☆11Sep 3, 2018Updated 7 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Dec 3, 2025Updated 2 months ago
- whole genome MLST analysis☆51Updated this week
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- Identification of structural variations☆12Jul 22, 2022Updated 3 years ago