Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
☆112Jan 30, 2026Updated 3 months ago
Alternatives and similar repositories for mikado
Users that are interested in mikado are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Splice junction analysis and filtering from BAM files☆42Mar 31, 2022Updated 4 years ago
- Robust Eukaryotic Annotation Toolkit☆17Feb 28, 2025Updated last year
- Multi-sample transcriptome assembly from RNA-Seq☆25Jun 10, 2018Updated 7 years ago
- This is the standalone version of the EviAnn pipeline☆144Apr 24, 2026Updated last week
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 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.
- Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement☆84Dec 3, 2025Updated 5 months ago
- source code for EVM☆124Nov 29, 2024Updated last year
- ☆188May 22, 2025Updated 11 months ago
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆77Aug 30, 2016Updated 9 years ago
- Ploidy agnostic phasing pipeline and algorithm☆49Jan 3, 2024Updated 2 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆215Mar 20, 2026Updated last month
- Taxon-aware analysis of clustered protein sequences☆31Jul 1, 2024Updated last year
- ☆42May 19, 2025Updated 11 months ago
- A genome completeness evaluation tool based on miniprot☆239Sep 18, 2025Updated 7 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆148Apr 13, 2026Updated 3 weeks ago
- A program for assessing the T2T genome continuity and completeness☆95Feb 28, 2026Updated 2 months ago
- ☆31Mar 3, 2026Updated 2 months ago
- Tool for globally phasing diploid assembly graphs with orthogonal data☆43Nov 25, 2024Updated last year
- Repeat-aware polishing genomes assembled using HiFi long reads☆101Apr 7, 2026Updated 3 weeks ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆205Nov 23, 2025Updated 5 months ago
- Python programs for processing GFF3 files☆104Dec 15, 2025Updated 4 months ago
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated 11 months ago
- Long Reads Annotation pipeline☆73Mar 31, 2022Updated 4 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆294Feb 25, 2026Updated 2 months ago
- Using Deep Learning to predict gene annotations☆286Mar 6, 2026Updated last month
- Yet another k-mer analyzer☆169Dec 30, 2025Updated 4 months ago
- PASA software☆200Feb 12, 2025Updated last year
- Iterative error correction of long reads☆13Dec 9, 2022Updated 3 years ago
- HELIANO is a software for detection and classification of Helitron-like elements.☆33Jun 10, 2025Updated 10 months ago
- Neural network classification of TE☆99Apr 3, 2026Updated last month
- Best practices and workflow for genome annotation☆79Apr 14, 2025Updated last year
- An accurate GFF3/GTF lift over pipeline☆535Aug 1, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆163Nov 4, 2025Updated 6 months ago
- TSEBRA: Transcript Selector for BRAKER☆49Apr 7, 2026Updated 3 weeks ago
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆457Apr 12, 2026Updated 3 weeks ago
- Align proteins to genomes with splicing and frameshift☆401Jan 5, 2026Updated 3 months ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆564Feb 14, 2024Updated 2 years ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆214Mar 9, 2026Updated last month
- De novo chromosome-level scaffolding and phasing tool using Hi-C☆30Nov 23, 2025Updated 5 months ago