Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools...1462 days ago
merqury: Evaluate genome assemblies with k-mers
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for in...1459 days ago
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 species. Unlike current coordinate lift-over tools whi...1289 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 genome in several hours and works with the California redwood genome...1285 days ago
GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.
...atasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies. https://www.biorxiv.org/cont...1242 days ago
307 days ago
QuasiModo - Quasispecies Metric Determination on Omics
This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant cal...1101 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, Assembly to Assembly Comparision tool: Comparative mapping between two genome as...1048 days ago
RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold merging1024 days ago
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 microbiome. While methods exist to identify...1012 days ago