Showing 28 open source projects for "bwa"

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  • Winningbidder.com provides free online auction software for nonprofits. Icon
    Our software is simple to use, allowing organizers to launch an auction in minutes. That doesn't mean it lacks features. Bidders enjoy max bidding, outbid notifications, and popcorn bidding.
  • Create the dream logo in a few clicks Icon
    Create the dream logo in a few clicks

    Explore a Wealth of Logo Options - Find Your Perfect Business Identity with Zoviz AI Brand Maker in Minutes.

    Zoviz AI Logo & Brand Kit Creator is a dynamic tool transforming branding processes for businesses of all sizes. This AI-driven platform simplifies logo creation and brand kit development, offering a user-friendly experience for both novices and professionals.
  • 1

    exome-test

    script for variant calling of Exome-Seq

    exome_test.sh is a shell script to run GATK best practice and varscan for variant-calling in exomseq. It uses bwa for alignment, UnifiedGenotyper and varscan to call variants, and Annovar to annotate. It also employs DepthofCoverage and BAM-readcount. [Notice] MAF files compatible with MutSigCV are added. The Annovar filter dbnsfp30a is updated. Correction of an error in the title line of merge file. -ni option added. -vb option (-B in varscan) added exac03nontcga is added. An error about...
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  • 2
    BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
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    Downloads: 374 This Week
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  • 3

    mirplant

    miRPlant: An Integrated Tool for Identification of Plant miRNA

    please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qimrberghofer.edu.au).
    Downloads: 3 This Week
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  • 4
    miRDeep*

    miRDeep*

    MiRDeep*

    Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction.
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    Downloads: 1 This Week
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  • BIGDBM is a leading provider of B2B data Icon
    BIGDBM is a leading provider of B2B data

    For marketing companies, sales organizations, data providers, e-commerce stores

    Unlock significant value in your marketing campaigns, lead generation strategies, and identity verification workflows with our leading US consumer and B2B datasets. Our unrivaled consumer datasets provide you with valuable consumer insights including lifestyle attributes, buyer intent, and consumer website visits. Explore our B2B dataset for comprehensive and up-to-date contact data on US companies and professionals to build your sales pipeline. Trust our identity data for accurate identity verification to ensure platform trust and compliance.
  • 5

    BWA-X

    BlackWolf Aerospace Experimental Mod Repo for Kerbal Space Program Mods

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  • 6
    BarraCUDA Fast Short Read Aligner
    Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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    Downloads: 1 This Week
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  • 7
    SPANDx

    SPANDx

    Comparative analysis of haploid next-generation genome sequence data

    SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A...
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  • 8

    VoltMR

    Pure java NGS mapping soft run on Hadoop 2.0

    VoltMR is pure java NGS (DNA/RNA) mapping and realignment soft that run on Hadoop 2.0 The accuracy is comparable to BWA-MEM and novoalgin with speed faster than those aligner. Using 100 core, VoltMR finish typical exome sample (10GB),mapping, sort, mark duplicate, local realignment in 30 minitue. It use about 10GB to 15GB RAM for each hadoop mapper and reducer. Currently, VoltMR take fastq as a input and output bam/ADAM format. For DNA mapping, GATK compatible realignment/recalbration...
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  • 9
    converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.
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  • Case Management Software for Nonprofits Icon
    Case Management Software for Nonprofits

    CharityTracker offers easy-to-use case management software for nonprofits, helping them track assistance, measure outcomes, and generate reports.

    A case management CRM that focuses on your clients, to measure real-world impact, not just data. Your Day Just Got Shorter - We know you’re busy and don’t have time for complicated software – We’ve changed that! Even your staff will enjoy using the system – No more headaches and missing data from reports so you can use your valuable time to serve more people. CharityTracker is a cloud-based, HIPAA compliant software that’s easy to use for nonprofits of all sizes. With no setup fees, hidden fees, or contracts, you can cancel anytime! Our time saving solution provides a secure way to streamline how you manage cases, record case notes & assistance, create reports, collaborate, set goals, measure outcomes, make referrals & prove your impact with change-over-time reports for your funders. We're at work in 2,200 communities! Book a free demo. Pricing starts at just $20/mo. user
  • 10

    MIPVAR

    MIP VARiant calling tool

    A Java application to analyse Molecular Inversion Probe sequencing data within short time. Running the pipeline requires previous installation of three general tools: BWA, GATK and Bedtools. Input: For running the pipeline you need to specify 3 arguments. An example of the command is given below. The two input files are essential to specify the sample and run configuration. The environment argument should always be set to EMPTY. A brief description of other required files can be found...
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  • 11

    Faligner

    Faligner: a Local Sequence Alignment Ubuntu Package

    A package based on 3 local alignment tools i.e., Bowtie, Bowtie2 and BWA. Package covers single-end, paired-end alignments. Moreover, the package also demonstrates overlap alignment and colorspace alignment features. The package also includes graphical user interface to make it interactive.
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  • 12

    MutAid

    MutAid: Sanger and NGS based pipeline for mutation screening.

    ..., variant calling, variant annotation and co-analyze Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as deletions and insertions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms (Sanger, Illumina, 454 and Ion Torrent) and five read mappers including BWA,TMAP, Bowtie,Bowtie2 and GSNAP and four variant callers
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  • 13
    CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads...
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  • 14

    SAMSVM

    A tool for misalignment filtration on SAM-format sequences with SVM

    Applying the LIBSVM, a package of support vector machine, SAMSVM was developed to correctly detect and filter the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis.
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  • 15

    BWA-MT

    A multi-thread version of BWA

    A multi-thread version of BWA supporting the samse alignment generation stage of BWA
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  • 16
    MICA-aligner

    MICA-aligner

    Next-generation sequencing short reads aligner based on Intel® MIC

    Latest Code in GitHub: https://github.com/aquaskyline/MICA-aligner To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core. Experiments on aligning 150bp paired-end reads show that MICA using one MIC board is ~4.85 times faster than the CPU-(multi-core)-based BWA-MEM and about the same speed as the GPU-based SOAP3-dp. Furthermore, MICA’s simplicity...
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  • 17
    SOAP3-DP

    SOAP3-DP

    Fast, Accurate and Sensitive GPU-based Short Read Aligner

    Latest Code on GitHub: https://github.com/aquaskyline/SOAP3-dp SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads...
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  • 18

    openSEQ

    NGS compute distro proloaded with pipeline analysis software

    ... 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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  • 19

    Listeria_pipe

    Pipeline for assembling Listeria monocytogenes illumina reads

    This pipeline will perform trimming and filtering of short-read sequence data, assemble with four reference-guided aligners (BWA, MOSAIK, Novoalign and SMALT) and perform local realignments around indels.
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  • 20
    Software quality assurance is essential in genomic medicine. Nonetheless there is currently no systematic evaluation of existing computational tools used for whole genome or whole exome sequencing data analysis. We developed a Metamorphic Testing tool that tests three widely used short-read alignment programs (BWA, Bowtie and Bowtie2) in order to systematically evaluate their performance.
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  • 21
    Seal

    Seal

    A toolkit for distributed processing of HT sequencing data.

    Seal is a Hadoop-based distributed short read alignment and analysis toolkit. Currently Seal includes tools for: read demultiplexing, read alignment, duplicate read removal, sorting read mappings, and calculating statistics for empirical base quality recalibration. Seal scales, easily handling TB of data.
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  • 22

    estMOI

    estimating Multiplicity Of Infection using short read sequence data

    estMOI is intended to estimate Multiplicity of Infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data as follows: INPUT files: estMOI requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. 1. Short reads are aligned to a reference genome using BWA...
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  • 23
    Parallel implementation of BWA (http://bio-bwa.sourceforge.net/) using the OpenMPI library.
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  • 24
    Standard chart of accounts ("Standardkontenrahmen") as needed by accounting software to meet German requirements. Includes tax automatics, data for creating "Umsatzsteuervoranmeldung", "BWA", "GuV" and "Bilanz" and utils for different accounting software.
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  • 25

    CGAP-Align

    A new time efficient read alignment tool built on the top of BWA

    See Wiki page for details.
    Downloads: 0 This Week
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