Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. I...es). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can th...2038 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage exe..._read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple short read files. Removed use of configuratio...2081 days ago
KAST: Perform Alignment-free k-tuple frequency comparisons from sequences
Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.2067 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space an...2053 days ago
2053 days ago
vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow easy manipulation and visualization of varia...format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R...2032 days ago
pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig bed (many options) bedgraph links (represented as arcs) Hi-C matrices (if HiCExplorer is installed)2017 days ago
AMStat: display statistics of large sequence files from next generation sequencing projects
SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported f...2017 days ago
BamView: a free interactive display of read alignments in BAM data files
To run the application on UNIX from the downloaded jar...n when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the comma...the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in...2017 days ago
Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded O...nopolish. Deepbinner can demultiplex the fast5 fileswhich makes this easier....You only have basecalled reads not the raw fast5 files (which Deepbinner requires)....1999 days ago