genomic-medicine-sweden / jasenLinks
Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
☆11Updated this week
Alternatives and similar repositories for jasen
Users that are interested in jasen are comparing it to the libraries listed below
Sorting:
- Scaffolding with assembly likelihood optimization☆22Updated 4 years ago
- consensus approach for community profiling with nanopore amplicon sequencing data☆14Updated 8 months ago
- Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories☆14Updated 2 months ago
- transposable element typing pipeline☆18Updated last year
- Find Unique genomic Regions☆30Updated 3 months ago
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆33Updated last week
- ☆15Updated 7 years ago
- ☆14Updated last year
- easy_sbatch - Batch submitting Slurm jobs with script templates☆17Updated 3 years ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Updated last year
- Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files☆21Updated 2 years ago
- MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…☆14Updated 2 years ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- Rapid discovery of reciprocal best blast pairs.☆10Updated 7 months ago
- A nextflow version of the Wochenende reference metagenome binning and visualization pipeline☆14Updated 6 months ago
- WGS (Wheat) Robust Assembly Pipeline☆22Updated 3 years ago
- Convert genbank files to a swath of other formats☆18Updated last year
- Detect iSNV and construct whole viral genomes from metagenomic samples☆15Updated this week
- Quality control plotting for long reads☆10Updated last year
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 2 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆24Updated last year
- Fast and scalable nanopore adaptive sampling☆34Updated 2 years ago
- A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research☆16Updated this week
- Population-wide Deletion Calling☆35Updated 2 months ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆11Updated 6 months ago
- Nanopore plasmid pipeline (FAST5 basecalling, assembly, plasmid identification and antimicrobial resistance genes identification).☆12Updated 4 years ago
- interactive Multi Objective K-mer Analysis☆23Updated 2 years ago
- ClaMSA (Classify Multiple Sequence Alignments).☆13Updated 7 months ago
- A comparative genome scaffolding tool☆17Updated 6 years ago
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆11Updated last month