reference-free transcriptome assembly for short and long reads
☆108Jan 28, 2024Updated 2 years ago
Alternatives and similar repositories for RNA-Bloom
Users that are interested in RNA-Bloom are comparing it to the libraries listed below
Sorting:
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆40Jan 7, 2026Updated last month
- A genome completeness evaluation tool based on miniprot☆235Sep 18, 2025Updated 5 months ago
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆22Jan 21, 2026Updated last month
- PSAURON is a machine learning model for rapid assessment of protein coding gene annotation☆54Dec 11, 2025Updated 2 months ago
- reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graph☆18Jul 26, 2023Updated 2 years ago
- De novo construction of isoforms from long-read data☆35Jun 10, 2025Updated 8 months ago
- ☆89Dec 3, 2025Updated 3 months ago
- PECAT, a phased error correct and assembly tool☆59Dec 8, 2025Updated 2 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
- FastOMA is a scalable software package to infer orthology relationship.☆90Updated this week
- Ploidy agnostic phasing pipeline and algorithm☆49Jan 3, 2024Updated 2 years ago
- This is the official site for JASPER (Jellyfish based Assembly Sequence Polisher for Error Reduction)☆12Jun 27, 2024Updated last year
- Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation☆181Dec 16, 2025Updated 2 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆262Jul 12, 2025Updated 7 months ago
- This is the standalone version of the EviAnn pipeline☆139Feb 5, 2026Updated last month
- Linear-time de novo Long Read Assembler☆41Oct 22, 2025Updated 4 months ago
- source code for EVM☆122Nov 29, 2024Updated last year
- Full-length transcriptome splicing and mutation analysis☆86Jun 24, 2024Updated last year
- Finding putative exons and constructing splicegraphs using Trans-ABySS contigs☆11Nov 8, 2018Updated 7 years ago
- JTK -- a regional diploid genome assembler☆25Oct 20, 2024Updated last year
- Error correction of ONT transcript reads☆58Sep 6, 2023Updated 2 years ago
- SUPPA: Fast quantification of splicing and differential splicing☆293Nov 6, 2025Updated 3 months ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆141Apr 6, 2025Updated 10 months ago
- Improved long-read assembly by preserving contained reads☆30Aug 22, 2024Updated last year
- Consensus genome annotation using OMA☆31Jan 14, 2026Updated last month
- Transcript assembly and quantification for RNA-Seq☆489Dec 26, 2025Updated 2 months ago
- CoalHMM☆22Nov 4, 2013Updated 12 years ago
- chloroplast genome assembly using long reads data☆14Jul 8, 2025Updated 7 months ago
- De novo clustering of long transcript reads into genes☆19Dec 15, 2025Updated 2 months ago
- Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).☆104Jul 23, 2024Updated last year
- A program for assessing the T2T genome continuity☆92Dec 14, 2025Updated 2 months ago
- A deep learning-based SNP calling method to identify SNPs based on low-coverage Nanopore sequencing reads.☆21Nov 20, 2022Updated 3 years ago
- A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models☆18Nov 29, 2022Updated 3 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆210Jan 30, 2026Updated last month
- Genome size estimation from long read overlaps☆81Updated this week
- Genome mapping and spliced alignment of cDNA or amino acid sequences☆110Updated this week
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Aug 24, 2022Updated 3 years ago
- Quality assessment of de novo transcriptome assemblies from RNA-Seq data☆26Nov 14, 2025Updated 3 months ago
- Tool for the Quality Control of Long-Read Defined Transcriptomes☆252Feb 24, 2026Updated last week