cidgoh / bacpaqLinks
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
☆11Updated 2 months ago
Alternatives and similar repositories for bacpaq
Users that are interested in bacpaq are comparing it to the libraries listed below
Sorting:
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆23Updated 3 weeks ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated 2 years ago
- Microbial agile accurate SNP Typer☆30Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆27Updated 3 weeks ago
- Quality control plotting for long reads☆10Updated last year
- Influenza genome analysis Nextflow workflow☆28Updated last week
- A pipeline for whole genome assembly☆16Updated 3 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Influenza genome analysis Nextflow workflow☆23Updated last week
- a broadly applicable tool for automated gene identification and retrieval☆32Updated 8 months ago
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years ago
- Intra-species bacterial contamination detection☆25Updated 6 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Updated 4 years ago
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆33Updated last month
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆61Updated 11 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆41Updated 2 months ago
- Detect iSNV and construct whole viral genomes from metagenomic samples☆21Updated last week
- Correcting errors in noisy long reads using variation graphs☆51Updated 2 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated 5 months ago
- Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.☆17Updated 6 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 3 weeks ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆37Updated 4 months ago
- A script for comparing old vs new versions of genome annotations☆21Updated 2 years ago
- screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics☆11Updated 4 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated last year
- Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files☆21Updated 2 years ago
- An R package to infer and analyze synteny networks from protein sequences☆30Updated 2 weeks ago
- Within-species genome-wide dN/dS estimation from very many genomes☆21Updated 4 years ago