Search Results for "bam-readcount"
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Showing 55 open source projects for "bam-readcount"
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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should... -
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Pandora FMS: Flexible Monitoring System
Open Source Monitoring System for performance and availability.
Pandora FMS is an enterprise-ready monitoring solution that provides unparalleled flexibility for IT to address both immediate and unforeseen operational issues, including infrastructure and IT processes. It uniquely enables business and IT to adapt to changing needs through a flexible and rapid approach to IT and business deployment. Pandora FMS consolidates all the needs of modern monitoring (ITOM, APM, BAM) and provides status and performance metrics from different operating systems... -
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rna-test
script for variant calling of RNA-Seq
rna_test.sh is a shell script to run GATK best practice for variant-calling in RNAseq. It uses STAR2.5 for alignment, HaplotypeCaller to call variants, and Annovar to annotate. It also employs STAR-Fusion, Cufflinks and Stringtie FPKM, HTSeq_count and BAM-readcount. Notice: STAR_gene_read and HTSeq_count are added. exac03nontcga is added. STAR-Fusion is added. Stringtie is added. Disable BQSR (-skb) opteion is added. New avsnp(150) is updated. use -dcov in SplitNCigarReads added... -
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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. -
Our robust pre-built connectors and our no-code, drag-and-drop interface makes it easy and fast to automatically sync vendors, invoices, and invoice payment data between Tipalti and your ERP or accounting software.
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crossmap
convert genome coordinates betweeen assemblies
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format. -
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
123FASTQ performs all the pre-processes of Illumina next-generation sequencing reads (FASTQ files) easier than ever. Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf Authors: Milad Eidi, Samaneh Abdolalizadeh, Mohammad Hossein Nassirpour Supervisors: Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ,... -
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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... -
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RNASeqBrowser
RNASeqBrowser: A genome browser for strand specific RNAseq reads
..., InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. j.an@qut.edu.au -
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Somatic APP analysis
Reanalysis of somatic APP retrotransposition
...: PRJNA577966 * The input bam should be mapped to APP751.fa (provided in the 'data' folder) and sorted by read name after mapping • Estimation of gencDNA fraction java -jar somaticAPP.jar -F -b input.bam -a BWA_PATH -s SAMTOOLS_PATH [optional_arguments] * Input data: PRJNA493258 * The input bam should be a human-genome-mapped (hg38), coordinate-sorted, and duplicate-marked file. Try -h or -? options to get detailed descriptions for optional input parameters -
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svdetectcnv.sh
shell script to run SVDetect with baseline adjustment
svdetectcnv.sh is a shell script to run SVDetect CNV mode. In addition to the original outputs of SVDetect, the script also outputs an adjusted bed.graph with baseline adjusted to the average Log2Ratio of a certain chromosome or all chromosomes, and a sorted density file. **Update*** New version uses the splitted bam produced by exome_test.sh and allows for multithreading to split bam. -
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hiddenDomains
hiddenDomains: a modern HMM to identify ChIP-seq enrichment
hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities. -
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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@qut.edu.au). -
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Niche Analyst (NicheA) was developed based on the BAM framework which allows users to create virtual spaces and virtual species, and to analyze ecological niches in both multivariate environmental and geographic spaces, linking views of the niche in the two spaces. The unique functionality in NicheA, not available in other software programs, is estimating Grinnellian niches of species based on environmental variables and occurrence records, but with a clear focus on fundamental ecological...
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meerkat.sh
script of SV calling in Exome-seq
meerkat.sh is a shell script to run Meerkat for SV detection in Exome-seq. The script accepts single BAM or paired tumor-normal BAMs. -
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge... -
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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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ITD-Assembler
A tool to detect mid sized tandem duplications
This tool uses de novo assembly to detect Tandem Duplications in next gen assembly data. it takes as an input a bam file and outputs results in a custom format. It is linux based and has been developed primarily in haskell, and some parts in C and python. -
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SeqPig
Use Apache Pig to process your large sequencing datasets!
SeqPig is a library for Apache Pig for the distributed analysis of large sequencing datasets. It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output. For more information see the manual at http://seqpig.sourceforge.net/ -
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MIPVAR
MIP VARiant calling tool
... in the example input files (see sampleConfigExample.txt and runConfigExample.txt). Run command: java -Dsnappy.disable=true -Dlogging.config=/path-to-pipeline/MIPVAR-<version>-package/conf/logback.xml -cp "/path-to-pipeline/MIPVAR-<version>-package/lib/*" org.umcn.gen.mip.pipeline.RunMIPPipeline -sampleConfig /path-to-file/sampleConfig.txt -environment EMPTY -overridePipelineConfig /path-to-file/runConfig.txt Output: - Bam files per sample - VCF - Coverages per MIP per Sample -
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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in... -
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and money...
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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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Telomerecat: The Telomere Computatioanl Analysis Tool Telomerecat allows you to generate average TL estimates for any high throughput paired end sequencing samples.
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
.... Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet. -
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jChIP
Graphical environment for exploratory ChIPSeq data analysis
jChIP is a GUI-based Java application for ChIP-Seq data analysis. It was created to build binding profiles between proteins and loci in the genome. In addition it computes statistics of the number of loci/positions containing specified amount of tags. jChIP is able to load data in several common formats (SAM, BAM, WIG, BED, Bowtie) and download loci definitions directly from the Ensembl database. http://www.biomedcentral.com/1756-0500/7/676