kishwarshafin / pepperView external linksLinks
PEPPER-Margin-DeepVariant
☆257Jan 12, 2024Updated 2 years ago
Alternatives and similar repositories for pepper
Users that are interested in pepper are comparing it to the libraries listed below
Sorting:
- ☆33Nov 6, 2022Updated 3 years ago
- Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling☆330Sep 25, 2025Updated 4 months ago
- Long read aligner☆114May 26, 2023Updated 2 years ago
- Long read / genome alignment software☆311Dec 16, 2025Updated last month
- Structural variant toolkit for VCFs☆397Jan 23, 2026Updated 3 weeks ago
- Pipeline to convert a haploid assembly into diploid☆111Jan 23, 2025Updated last year
- diploid SNV caller for error-prone reads☆206Apr 26, 2024Updated last year
- Structural variation caller using third generation sequencing☆634Dec 18, 2025Updated last month
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads☆274Oct 13, 2022Updated 3 years ago
- Plot structural variant signals from many BAMs and CRAMs☆558Jul 13, 2024Updated last year
- pbsv - PacBio structural variant (SV) calling and analysis tools☆162Feb 26, 2025Updated 11 months ago
- Sequence correction provided by ONT Research☆499Dec 8, 2025Updated 2 months ago
- ☆78Jun 12, 2020Updated 5 years ago
- Long read based human genomic structural variation detection with cuteSV☆278Sep 30, 2025Updated 4 months ago
- Read-based phasing of genomic variants, also called haplotype assembly☆404Dec 31, 2025Updated last month
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆105Jun 6, 2021Updated 4 years ago
- Toolset for SV simulation, comparison and filtering☆411Dec 1, 2023Updated 2 years ago
- ☆119Oct 10, 2025Updated 4 months ago
- Variant calling tool for long-read sequencing data☆117Mar 19, 2025Updated 10 months ago
- Structural Variant Identification Method using Long Reads☆181Jun 29, 2021Updated 4 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆174Apr 12, 2024Updated last year
- Evaluate variant calls and its combination with k-mer multiplicity☆67Dec 2, 2022Updated 3 years ago
- ☆123Jan 21, 2026Updated 3 weeks ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆235Dec 29, 2023Updated 2 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- A PyTorch Basecaller for Oxford Nanopore Reads☆428Jan 14, 2026Updated last month
- Yet another k-mer analyzer☆158Dec 30, 2025Updated last month
- A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment☆87Apr 8, 2021Updated 4 years ago
- k-mer based assembly evaluation☆338Jun 28, 2024Updated last year
- software tools for haplotype assembly from sequence data☆226Feb 9, 2025Updated last year
- Nanopore raw signal repeat detection pipeline☆45Mar 17, 2023Updated 2 years ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 5 months ago
- DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) …☆255Mar 11, 2025Updated 11 months ago
- MarginPolish: Graph based assembly polishing☆47Nov 24, 2020Updated 5 years ago
- Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by a…☆205May 4, 2023Updated 2 years ago
- Sequence-to-graph mapper and graph generator☆470Aug 11, 2025Updated 6 months ago
- ☆84Mar 3, 2025Updated 11 months ago
- Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling☆105Sep 1, 2022Updated 3 years ago
- CLI tool for flexible and fast adaptive sampling on ONT sequencers☆194Apr 28, 2025Updated 9 months ago