SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local asse...e default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at t...1576 days ago
1566 days ago
1559 days ago
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.1525 days ago
Filtlong: quality filtering tool for long reads
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing whi...1512 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for insta...to find the bridging that cross the gap, and then fills the long read origi...1511 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS...ent-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair...1508 days ago
medaka: Sequence correction provided by ONT Research
medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads agai...1507 days ago
Genobuntu: Package for Next Generation Sequencing and Genome Assembly
Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. I...CGS Allpaths IDBA TAIPAN Edena SOAPdenovo Maq IDBA-UD No. of Reads present in the Ref. Seq. ART NGS Reads Simu...1507 days ago
sunbeam: A robust, extensible metagenomics pipeline
Sunbeam is a pipeline written in snakemake that simplifies and automates man...eployed on most Linux workstations and clusters. To read more, check out our paper in Microbiome. https://sunbeam.readthedoc...1476 days ago