a hidden Markov model to infer simple repeats from genome sequences
☆37Feb 19, 2021Updated 5 years ago
Alternatives and similar repositories for RepeatHMM
Users that are interested in RepeatHMM are comparing it to the libraries listed below
Sorting:
- ☆51Jun 25, 2024Updated last year
- A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data☆47Dec 6, 2024Updated last year
- Nanopore raw signal repeat detection pipeline☆45Mar 17, 2023Updated 2 years ago
- An accurate repeat detection from Nanopore data using deep learning and image techniques☆24Feb 28, 2023Updated 3 years ago
- A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.☆18Jan 16, 2026Updated last month
- Determining tandem repeat lengths using raw nanopore signals.☆15Sep 11, 2023Updated 2 years ago
- source code of the paper "RepLong - de novo repeat discovery from long reads"☆18Jan 4, 2025Updated last year
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 6 months ago
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 3 months ago
- Nanopanel2: a somatic variant caller for Nanopore panel sequencing data☆11Sep 21, 2021Updated 4 years ago
- Tools for the analysis of structural variation in genomes☆81Updated this week
- TREDPARSE: HLI Short Tandem Repeat (STR) caller☆25Aug 20, 2020Updated 5 years ago
- Structural variant caller for low-depth long-read sequencing data☆47Feb 5, 2026Updated 3 weeks ago
- DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications☆104Mar 8, 2023Updated 2 years ago
- Expanded STR algorithm for Illumina sequencing data☆23Sep 11, 2022Updated 3 years ago
- Dynamic time warping of Oxford Nanopore squiggle data to characterize tandem repeats.☆32Jul 2, 2020Updated 5 years ago
- Mark duplicate reads from PacBio sequencing of an amplified library☆12Feb 26, 2025Updated last year
- Archived version 1.0.2☆16Nov 25, 2019Updated 6 years ago
- Detect novel (and reference) STR expansions from short-read data☆70Dec 6, 2025Updated 2 months ago
- Accurate Typing of Human Leukocyte Antigen (HLA) by Oxford Nanopore Sequencing☆17Jan 19, 2018Updated 8 years ago
- ☆15Aug 22, 2023Updated 2 years ago
- Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation☆23Mar 4, 2019Updated 6 years ago
- Tandem repeat genotyping and visualization from PacBio HiFi data☆133Dec 8, 2025Updated 2 months ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- Toolkit for calling and analyzing de novo STR mutations☆17Dec 17, 2023Updated 2 years ago
- A tool for visualizing alignments of reads in regions containing tandem repeats☆90Dec 19, 2023Updated 2 years ago
- Noise-Cancelling Repeat Finder☆27Apr 11, 2023Updated 2 years ago
- Python bindings to minimap2☆16Sep 18, 2017Updated 8 years ago
- Derives consensus sequences from a set of long noisy reads by clustering and error correction.☆16Jul 20, 2021Updated 4 years ago
- Plot CNV data with a genome viewer in R☆15Apr 5, 2017Updated 8 years ago
- A python program to call methylation (m6A in DNA) from nanopore signal data☆47Jun 24, 2021Updated 4 years ago
- NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data☆20Jan 13, 2026Updated last month
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆59Jun 30, 2017Updated 8 years ago
- Long read based human genomic structural variation detection with cuteSV☆278Sep 30, 2025Updated 5 months ago
- TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain☆33Jun 17, 2024Updated last year
- Toolkit for genome-wide analysis of tandem repeats☆59Feb 19, 2026Updated last week
- A method for variant graph genotyping based on exact alignment of k-mers☆87Apr 1, 2019Updated 6 years ago
- Public Benchmark of Long-Read Structural Variant Caller on ONT PromethION Data☆14Nov 28, 2019Updated 6 years ago
- ☆10Jun 9, 2020Updated 5 years ago