Ultra-fast de novo assembler using long noisy reads
☆137Feb 24, 2021Updated 5 years ago
Alternatives and similar repositories for smartdenovo
Users that are interested in smartdenovo are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly☆533Sep 27, 2023Updated 3 years ago
- A single molecule sequence assembler for genomes large and small.☆707Sep 10, 2026Updated last month
- Nanopore data assembler☆171Mar 27, 2022Updated 4 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…☆303May 9, 2024Updated 2 years ago
- Pilon is an automated genome assembly improvement and variant detection tool☆391Apr 10, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A fuzzy Bruijn graph approach to long noisy reads assembly☆39Mar 15, 2017Updated 9 years ago
- Fast and accurately polish the genome generated by long reads.☆247Jan 9, 2025Updated last year
- Fast and accurate de novo assembler for long reads☆407May 10, 2024Updated 2 years ago
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆360Jul 19, 2025Updated last year
- Mummer alignment tool☆578Feb 4, 2025Updated last year
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads☆273Oct 13, 2022Updated 4 years ago
- calling SVs from Blasr contig level alignments☆54Mar 9, 2018Updated 8 years ago
- De novo assembler for single molecule sequencing reads using repeat graphs☆954Apr 3, 2026Updated 6 months ago
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆56Jun 18, 2026Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads☆111Oct 2, 2020Updated 6 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- A program to call variants from genome alignment☆84Apr 29, 2025Updated last year
- ONT assembly and Illumina polishing pipeline☆87Dec 8, 2020Updated 5 years ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆213Nov 18, 2022Updated 3 years ago
- haplotypic duplication identification tool☆298Oct 30, 2025Updated 11 months ago
- k-mer based assembly evaluation☆356Jul 6, 2026Updated 3 months ago
- The MARVEL assembler☆80Jul 7, 2023Updated 3 years ago
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆422Aug 25, 2026Updated 2 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- 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…☆310Mar 18, 2024Updated 2 years ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆818May 31, 2026Updated 4 months ago
- 3D de novo assembly (3D DNA) pipeline☆232Nov 29, 2023Updated 2 years ago
- A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long…☆67Jul 23, 2020Updated 6 years ago
- The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)☆81Oct 12, 2018Updated 8 years ago
- ☆278Jun 26, 2025Updated last year
- SMRT-SV: Structural variant and indel caller for PacBio reads☆28Feb 21, 2019Updated 7 years ago
- Signal-level algorithms for MinION data☆601Aug 5, 2023Updated 3 years ago
- Sequence-to-graph mapper and graph generator☆492Aug 11, 2025Updated last year
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Yet another k-mer analyzer☆178Dec 30, 2025Updated 9 months ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆220Jun 30, 2026Updated 3 months ago
- FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON…☆204Mar 4, 2022Updated 4 years ago
- Reference-free profiling of polyploid genomes☆149Oct 2, 2025Updated last year
- Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆127Apr 7, 2021Updated 5 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆245Dec 29, 2023Updated 2 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆180Oct 20, 2024Updated 2 years ago