Results for "BAM"
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vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. Th...Tags: vcfR, Tools, variant, call, format, files, BAM, plot
2009 days ago
BamView: a free interactive display of read alignments in BAM data files
To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the command line with the '-a' option: java -mx512m -jar BamView.jar -a p...Tags: BamView, free, interactive, display, read, alignments, BAM, data, files
1994 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a distribution of proportion of bases covered at or above...Tags: mosdepth, fast, BAM, CRAM, depth, calculation, WGS, exome, target, sequencing
1622 days ago
- Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions. Consed is compatible wi...
Tags: Consed, Finishing, Package, BAM, Viewer, Assembly, Editor, Autofinish, Autoreport, Autoedit, Align, Reads, Reference, Sequence
1539 days ago
tinycov: standalone command line utility written in python to plot coverage from a BAM file
Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user tinycov To install the development version: git clo...Tags: tinycov, standalone, command, line, utility, written, python, plot, coverage, BAM, file
1494 days ago
Quip: Aggressive compression of FASTQ, SAM and BAM files.
This will help us to reduce the amount of drive space we take up and decrease data transfer times Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as ...Tags: Quip, Aggressive, compression, FASTQ, SAM, BAM, files
702 days ago
- The key to finding a solution is to notice that most genomicsequences differ by very little. It may well be that the number of complete genome sequences being stored is increasing rapidly, but the actual amount of new data is very small. In other words, a single DNA sequence isn't particular...
Tags: data compression, genomics, sequencing, redundancy, repeats, bam, sff, gz, zip
3910 days ago
