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Mabs, a genome assembly tool which optimizes parameters of Hifiasm and Flye
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
An Example of Subgenome Phasing for Complex Allopolyploidy
⛓ Correct misassemblies using linked AND long reads
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
A gap-closing software tool that uses long reads to enhance genome assembly.
HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C
A collection of tools for Genome Assembly analysis
A novel genome assembly pipeline based on deep learning
Earl Grey: A fully automated TE curation and annotation pipeline
De novo assembler for single molecule sequencing reads using repeat graphs
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Transcript assembly and quantification for RNA-Seq
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Extract 3'UTR, 5'UTR, CDS, Promoter, Genes, Introns, Exons from GTF files
Pilon is an automated genome assembly improvement and variant detection tool
🌺 reference-free transcriptome assembly for short and long reads
Fast and accurate de novo assembler for long reads
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
starfish: a modular toolkit for giant mobile element annotation
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Quantification of transposable element expression using RNA-seq
A Nextflow workflow to generate lift over files for any pair of genomes
To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
TEtrimmer: a novel tool to automate manual curation of transposable elements
