jts / sga
de novo sequence assembler using string graphs
☆239Updated 5 years ago
Alternatives and similar repositories for sga:
Users that are interested in sga are comparing it to the libraries listed below
- lumpy: a general probabilistic framework for structural variant discovery☆319Updated 2 years ago
- Count bases in BAM/CRAM files☆312Updated 3 years ago
- A tool set for short variant discovery in genetic sequence data.☆195Updated 3 years ago
- Pilon is an automated genome assembly improvement and variant detection tool☆347Updated 2 years ago
- Reads simulator☆269Updated 3 years ago
- GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…☆180Updated 5 years ago
- A minimap2 frontend for PacBio native data formats☆181Updated 2 months ago
- VarDict☆192Updated last year
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆202Updated 2 years ago
- pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…☆274Updated 4 months ago
- Genome Assembly and Annotation Service code☆207Updated last year
- A tool to circularize genome assemblies☆236Updated 10 months ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆209Updated 4 years ago
- 3D de novo assembly (3D DNA) pipeline☆207Updated last year
- a toolkit for working with Oxford nanopore data☆242Updated 2 years ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆245Updated 8 months ago
- Ultra-fast de novo assembler using long noisy reads☆131Updated 3 years ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆227Updated 3 years ago
- Structural variation and indel detection by local assembly☆240Updated 3 months ago
- NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…☆296Updated 11 months ago
- PASA software☆183Updated last week
- Toolset for SV simulation, comparison and filtering☆371Updated last year
- Generate an interactive dot plot from mummer or minimap alignments☆195Updated last year
- PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.☆261Updated 2 weeks ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆172Updated 3 years ago
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆156Updated last year
- Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads☆203Updated 3 months ago
- SV detection from paired end reads mapping☆117Updated 5 years ago
- Bayesian genotyper for structural variants☆127Updated 3 years ago
- (Not Offical) BBMap short read aligner, and other bioinformatic tools.☆219Updated 4 years ago