Search Results for "bwa mac"

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.

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...

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@qut.edu.au).

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...

converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.

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...

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.

... mapping, 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...

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.

Parallel implementation of BWA (http://bio-bwa.sourceforge.net/) using the OpenMPI library.

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.

See Wiki page for details.

BioWebAuth (Biometrics for Web Authentication) is an open source Java framework intended to provide single sign-on web authentication based on BioAPI-compliant biometric software or devices. It uses the JA-SIG Central Authentication Service architecture.

A tool to analyse Java programs in order to show if and where they employ “busy waiting".