karel-brinda / Phylign
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
β27Updated 10 months ago
Alternatives and similar repositories for Phylign:
Users that are interested in Phylign are comparing it to the libraries listed below
- Code to create a PRG from a Multiple Sequence Alignment fileβ23Updated 10 months ago
- Phylogenetic compression of extremely large genome collections [661k βππ²ππΆπ | BIGSIdata βπ°π΄ππΆπ | AllTheBact'23 βπ³π±ππΆπ]β21Updated 2 months ago
- Genome size estimation from long read overlapsβ48Updated 2 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenomeβ30Updated 3 weeks ago
- β13Updated 3 weeks ago
- β21Updated 4 months ago
- Colinear block visualisation toolβ30Updated last year
- Plasmid analysis using rearrangement distancesβ31Updated 3 months ago
- Contains the description of a file format to store kmers and associated valuesβ32Updated 2 years ago
- Differential k-mer analysisβ34Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.β50Updated 7 months ago
- Variant call verificationβ16Updated last month
- A pipeline for bioinformatics analysis of bacterial genomesβ19Updated 7 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.β27Updated this week
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomesβ15Updated 6 years ago
- A k-mer search engine for all Sequence Read Archive public accessionsβ20Updated 3 months ago
- Sketch-based surveillance platformβ13Updated 2 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.β21Updated this week
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/biβ¦β16Updated last year
- Get microbial sequence data easier and fasterβ28Updated 5 years ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomesβ38Updated 4 months ago
- Remove human reads from a sequencing runβ36Updated 4 months ago
- Optimal sequence-to-graph alignment with recombinationsβ28Updated this week
- Haplotype-aware genome assembly toolkitβ29Updated 5 years ago
- β41Updated 3 months ago
- mGEMS Genomic epidemiology with mixed samplesβ16Updated 5 months ago
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.β36Updated this week
- Extracts subgraphs or components from a graph in GFA formatβ23Updated 3 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCAβ30Updated 5 months ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.β22Updated this week