Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorith...1657 days ago
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly access...1616 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most gen...y available at https://github.com/gabaldonlab/haplotypo, and as a Docker image.1612 days ago
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RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the a...1596 days ago
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Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convo...fier, using many of the architectural advances that have proven successful in image clas...1559 days ago
Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo: https://vgteam.github.io/sequenceTubeMap/1529 days ago
SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:1555 days ago