nf-core / bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
☆53Updated 8 months ago
Alternatives and similar repositories for bactmap:
Users that are interested in bactmap are comparing it to the libraries listed below
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆40Updated 4 years ago
- Simple bacterial assembly and annotation pipeline☆65Updated last month
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆32Updated last month
- A pipeline to investigate horizontal gene transfer from NGS data☆24Updated last month
- ☆26Updated last month
- Correct and scaffold assemblies using long reads☆47Updated last year
- whole genome MLST analysis☆40Updated 8 months ago
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆38Updated last month
- ☆30Updated last month
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆28Updated 2 weeks ago
- Three bacterial GWAS methods all rolled into one easy-to-use R package☆19Updated 9 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆55Updated last year
- Split k-mer analysis – version 2☆73Updated this week
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 3 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆41Updated last month
- Graph-based assembly phasing☆69Updated 2 months ago
- A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…☆96Updated this week
- k-mer learning materials☆48Updated 9 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- PacBio BAM toolkit☆39Updated 2 months ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆33Updated this week
- Gene-flank analysis tool☆26Updated last month
- Read Assembly and Annotation Pipeline Tool☆56Updated 3 months ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- TAXnomic Profile Aggregation and STAndardisation☆34Updated 2 months ago
- A tool for removing redundant genomes from a set of assemblies☆70Updated last year
- ☆13Updated 4 months ago