Liftoff: An accurate GFF3/GTF lift over pipeline
Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related...1274 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human g...1270 days ago
Breedbase is a comprehensive breeding management and analysis software
Breedbase is a comprehensive breeding management and analysis software. It can be used to de...ore large amounts of high density genotypic information, and provide Genomic Selection related...1256 days ago
IVA: accurate de novo assembly of RNA virus genomes
IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human i...1089 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the seq...variants. Some of the early attempts to do this well have been accomplished on human m...1086 days ago
Kmer: a suite of tools for DNA sequence analysis
More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assem...Sim4db: Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related...1033 days ago
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WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human m...997 days ago