amkram / shusherLinks
Private, browser-based placement of genome sequences on phylogenetic trees using UShER.
☆11Updated last year
Alternatives and similar repositories for shusher
Users that are interested in shusher are comparing it to the libraries listed below
Sorting:
- ☆14Updated 2 weeks ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆15Updated 8 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Updated 2 years ago
- Methods to determine sequence element (unitig) presence/absence☆23Updated 2 months ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi …☆18Updated 2 years ago
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆21Updated 2 months ago
- software to identify primers that can distinguish genomes☆20Updated 2 weeks ago
- Basecalling configuration prediction through FASTQ files☆32Updated 2 months ago
- A novel method for sequence similarity estimation☆28Updated last year
- Variant call verification☆16Updated 9 months ago
- Computation of average nucleotide identity with the use of MMseqs2☆15Updated last year
- HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…☆12Updated last year
- Sketch phylogenetic trees and networks☆24Updated last week
- Better Alignments with Translated HMMER☆24Updated this week
- metagenome population recombination rate estimation pipeline☆12Updated 2 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆39Updated last year
- ☆15Updated 8 months ago
- Manipulate and generate figures for trees in Newick format☆22Updated 6 months ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆24Updated 3 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆18Updated this week
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆18Updated 2 months ago
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Updated last year
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12Updated last year
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated 5 months ago
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17Updated 2 years ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Updated last week
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Updated last year
- Simple-to-use interactive comparison of two bacterial genomes☆22Updated last week
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆36Updated last month