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.
☆108Jan 30, 2026Updated last month
Alternatives and similar repositories for mikado
Users that are interested in mikado are comparing it to the libraries listed below
Sorting:
- Splice junction analysis and filtering from BAM files☆41Mar 31, 2022Updated 3 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☆139Feb 5, 2026Updated 3 weeks ago
- Ploidy agnostic phasing pipeline and algorithm☆49Jan 3, 2024Updated 2 years ago
- source code for EVM☆122Nov 29, 2024Updated last year
- ☆28Dec 1, 2022Updated 3 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆210Jan 30, 2026Updated last month
- ☆186May 22, 2025Updated 9 months ago
- Taxon-aware analysis of clustered protein sequences☆31Jul 1, 2024Updated last year
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆77Aug 30, 2016Updated 9 years ago
- ☆41May 19, 2025Updated 9 months ago
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- Long Reads Annotation pipeline☆73Mar 31, 2022Updated 3 years ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆203Nov 23, 2025Updated 3 months ago
- Python programs for processing GFF3 files☆103Dec 15, 2025Updated 2 months ago
- A genome completeness evaluation tool based on miniprot☆235Sep 18, 2025Updated 5 months ago
- Iterative error correction of long reads☆13Dec 9, 2022Updated 3 years ago
- A program for assessing the T2T genome continuity☆92Dec 14, 2025Updated 2 months ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆292Feb 25, 2026Updated last week
- Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement☆79Dec 3, 2025Updated 3 months ago
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆148Jan 27, 2025Updated last year
- ☆29Feb 5, 2026Updated 3 weeks ago
- Repeat-aware polishing genomes assembled using HiFi long reads☆98Nov 12, 2025Updated 3 months ago
- An accurate GFF3/GTF lift over pipeline☆530Aug 1, 2023Updated 2 years ago
- TSEBRA: Transcript Selector for BRAKER☆49Nov 14, 2025Updated 3 months ago
- 🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies☆122Feb 24, 2026Updated last week
- Tool for globally phasing diploid assembly graphs with orthogonal data☆43Nov 25, 2024Updated last year
- ☆86Jul 12, 2024Updated last year
- Best practices and workflow for genome annotation☆79Apr 14, 2025Updated 10 months ago
- Align proteins to genomes with splicing and frameshift☆395Jan 5, 2026Updated last month
- High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.☆67Aug 16, 2023Updated 2 years ago
- Neural network classification of TE☆97Oct 9, 2025Updated 4 months ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆558Feb 14, 2024Updated 2 years ago
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆159Nov 4, 2025Updated 4 months ago
- Fast genome analysis from unassembled short reads☆313Apr 8, 2024Updated last year
- Scaffolding of genomic assemblies with RNA seq data☆15Oct 8, 2015Updated 10 years ago
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated 9 months ago
- Using Deep Learning to predict gene annotations☆276Feb 25, 2026Updated last week