jolespin / pykofamsearchLinks
Fast implementation of KofamScan optimized for high-memory systems using PyHMMER
☆12Updated 2 weeks ago
Alternatives and similar repositories for pykofamsearch
Users that are interested in pykofamsearch are comparing it to the libraries listed below
Sorting:
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆18Updated 7 months ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆23Updated 2 weeks ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 2 weeks ago
- codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the…☆12Updated last week
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 3 months ago
- ☆24Updated 6 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 2 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- ☆10Updated last month
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆37Updated 4 months ago
- Genome size estimation from long read overlaps☆59Updated 2 weeks ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆76Updated 2 weeks ago
- Python implementation of barrnap (Bacterial ribosomal RNA predictor)☆21Updated 6 months ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆15Updated 10 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated last week
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 5 years ago
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆46Updated last week
- lsaBGC - suite for pan-BGC-omics analysis☆19Updated last week
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆25Updated 2 weeks ago
- Plasmid analysis using rearrangement distances☆45Updated 2 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆48Updated last week
- MetagenOmic read Re-Assigner and abundance quantifier☆19Updated 6 months ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆36Updated last year
- Computation of average nucleotide identity with the use of MMseqs2☆13Updated 7 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago