bluenote-1577 / floria
Strain-level haplotyping for metagenomes with short or long-reads.
☆51Updated 3 weeks ago
Alternatives and similar repositories for floria:
Users that are interested in floria are comparing it to the libraries listed below
- Genome size estimation from long read overlaps☆55Updated 3 weeks ago
- A pipeline for bioinformatics analysis of bacterial genomes☆28Updated this week
- Recombination-free trees☆58Updated last month
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated last week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated 2 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Remove human reads from a sequencing run☆40Updated 7 months ago
- Bacterial GWAS analysis☆40Updated 2 weeks ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆34Updated last month
- Colinear block visualisation tool☆30Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 6 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated last week
- reference-based long read assemblies of bacterial genomes☆48Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- Plasmid analysis using rearrangement distances☆42Updated 5 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆25Updated 2 weeks ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 7 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 9 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆30Updated last month
- Evaluating Nanopore-based bacterial variant calling☆18Updated 4 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated 2 years ago
- Jaeger is a quick and precise tool for detecting phages in sequence assemblies.☆30Updated this week
- strain-level analysis tools☆36Updated 6 months ago
- plasmidVerify: plasmid contig verification tool☆13Updated 5 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 3 weeks ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆34Updated last week
- Gene-flank analysis tool☆27Updated 4 months ago
- Microbial agile accurate SNP Typer☆29Updated last year