Search Results for "picard"
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Showing 9 open source projects for "picard"
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Fusion Detection Pipeline
Fusion gene detection pipeline bundled into a Singularity container.
... by Picard Tools for calculation of our filtering metrics: Fusion Transcript Score (FTS). Further filtering is realized by a custom blacklist, our Promiscuity Score (PS) and Robustness Score (RS). Identified fusion genes are reported with evidence levels based on our filtering. This pipeline has been developed and optimized in a study of 806 AML patient samples (https://doi.org/10.3324/haematol.2021.278436). -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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Car Stereo MP3 Sort
Sorts MP3 files for Linux users' car stereos
Car stereos often list music by FAT32 entries, metadata, or timestamp, which this script corrects. Specifically, this script does three things to a detected USB or SD card: 1 Recursively sets the date of all FAT directories and files to the current time. #2 Sorts the FAT file system to match the names of the files and folders. #3.Offers Picard to perform other tasks with your music, such as downloading album art. -
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WODA solver
A finite volume groundwater simulator
WODA (Well Outline and Design Aid) is a groundwater simulator developed at the Group for Numerical Analysis, Jaroslav Cerni Institute, Belgrade, Serbia. WODA does not have its own graphical user interface, but it can work with groundwater models constructed using the freely available Lizza interface, http://www.bioirc.ac.rs/index.php/groundwater-flow-software. -
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mlrip
High quality CD music ripper for Linux, with Musicbrainz tag support
mlrip uses secure ripping (multiple rips which are compared) to ensure the best copy of the CD audio, with Musicbrainz integration to ensure best idenification and tagging of ripped music. Music can be ripped to flac and mp3 although other formats can easily be added. -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877...
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openSEQ
NGS compute distro proloaded with pipeline analysis software
.... The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk -
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NKA
Nonlinear Krylov acceleration of fixed-point and Newton-like methods
Nonlinear Krylov Acceleration (NKA) is a method for accelerating the convergence of fixed-point (Picard) iterations. Many Newton-like and inexact Newton methods are fixed point iterations. The NKA project provides the canonical implementation of the method for several programming languages. The black-box accelerator is simple to integrate into existing code. Placed in the iteration loop, it observes the sequence of solution updates and replaces them with improved updates using information... -
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BAMStats is a GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.
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