LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
...can be set by --long_read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple short read files. Removed use of configurati...2095 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.2081 days ago
vcfR: a package to manipulate and visualize VCF data in R
...(VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into...f genomic data. Once processing is complete data may be written to a VCF file or converted into other popul...2046 days ago
Scribl : HTML5 canvas genomics graphic library
Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.2046 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
...nd a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of...2041 days ago
BamView: a free interactive display of read alignments in BAM data files
...on on UNIX from the downloaded jar file run the UNIX: java -mx512m -...ed: java -jar BamView.jar -h BAM files can be specified on the comm...-mx512m -jar BamView.jar -a pathToFile/sorted.bam If a BAM filename...e this easier BamView will read in files that contain a list of filen...2031 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
...h-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standard file formats. Building on Wha...2026 days ago
SISRS: Site Identification from Short Read Sequences
Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.2012 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.1997 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)1993 days ago