RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.1517 days ago
NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
...ents and various local differences. These features make NucDiff to be perfectly suitable to compare assemblies with each other or with available reference genomes. NucDiff provides in...1513 days ago
1489 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and t...1204 days ago
Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
...-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outpu...1456 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
...le genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios. SVEngine takes as input reference contigs in FASTA files, varia...1453 days ago
merqury: Evaluate genome assemblies with k-mers
...led individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of to...1453 days ago
proActiv: Estimation of Promoter Activity from RNA-Seq data
proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relat...1413 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
...rm about the consistency of contigs and bins, allowing to spot potential chimeras. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes...1409 days ago
parallelLastz: Lastz with multi-threads support.
...an reduce run time linearly, and use almost equal memory as the original lastz program. This is useful when you lastz a big query file to a huge reference like human whole genome seque...1404 days ago