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Fast genome analysis from unassembled short reads
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
A gap-closing software tool that uses long reads to enhance genome assembly. AB4A
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
A genomic k-mer counter (and sequence utility) with nice features.
Evaluation and polishing workflows for T2T genome assemblies
Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)
Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
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.
pbsv - PacBio structural variant (SV) calling and analysis tools
Structural Variant Identification Method using Long Reads
🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies