mgalardini / pyseerLinks
SEER, reimplemented in python 🐍🔮
☆125Updated 5 months ago
Alternatives and similar repositories for pyseer
Users that are interested in pyseer are comparing it to the libraries listed below
Sorting:
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆98Updated 5 months ago
- Create a tree using Mash distances☆172Updated 2 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆142Updated last year
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆129Updated last year
- Bioinformatics program inStrain☆177Updated 5 months ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆103Updated 7 months ago
- Metagenomic classification of long-read sequencing data☆95Updated last month
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆116Updated last year
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆112Updated last year
- viralVerify: viral contig verification tool☆72Updated 4 years ago
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆120Updated last month
- A toolbox for comparative genomics.☆105Updated 4 years ago
- VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies☆144Updated this week
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆78Updated 2 years ago
- Interactive quality assessment of genome assemblies☆113Updated 5 months ago
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆51Updated last year
- ☆84Updated 2 years ago
- Processing pipeline for pan-genome visulization and exploration☆141Updated 2 years ago
- A toolbox for pangenome analysis and threshold evaluation.☆101Updated 3 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆100Updated 2 months ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆124Updated 2 years ago
- Microbiome classification pipeline☆65Updated 5 months ago
- CLI tool to annotate genes with KOfam☆85Updated 2 years ago
- DDBJ Fast Annotation and Submission Tool☆83Updated last month
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆66Updated 2 years ago
- SKESA assembler☆123Updated last year
- Antibiotic resistance prediction in minutes☆112Updated 11 months ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆75Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago