Search Results for "bam-readcount" - Page 2
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Showing 84 open source projects for "bam-readcount"
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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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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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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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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 "Files"... -
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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, available...
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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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dupRadar
Quality control for PCR artefacts in RNA-Seq data
dupRadar is an R package which is part of the Bioconductor project . It requires mapped, duplicate marked RNA-Seq reads as a bam file and a gene annotation file in GTF format and produces a table with per gene values such as read counts, percentage of duplicate reads, normalized read counts. The package provides functions for plotting and analyzing the duplication rates dependent on the expression levels. Install it from R with: R> source("https://bioconductor.org/biocLite.R") R> biocLite... -
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sam_comp
Compression for SAM/BAM file format
This is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. -
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
... (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 -
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MNV Annotation Corrector
Multi-nucleotide Variation Annotation Corrector for NGS SNV callers
... of user-provided SNVs and the matching BAM file to accurately identify MNV, and use existing annotators (currently supports ANNOVAR/SnpEff/VEP) to provide corrected amino acid prediction. -
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
... from RNAseq data: preprocess: Generates aligned and recalibrated BAM files. expression: Generates gene expression (RPKM) and quality metrics. fusion: Identifies candidate gene fusions. guess-ft: Supervised search for fusion transcripts. guess-if: Supervised search for intragenic fusions. homology: Calculates homology between given two genes. frame: Predicts functional consequence of fusion transcript -
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SOAP3-DP
Fast, Accurate and Sensitive GPU-based Short Read Aligner
... with different lengths. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE 8(5): e65632. doi:10.1371/journal.pone.0065632 -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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mirUtils
miRNA alignment quantitation based on miRBase annotations
mirUtils provides quantitation of aligned microRNA sequences based on miRBase annotations. Starting from a miRBase-aligned BAM/SAM file, mirUtils reports counts and quality metrics for several taxonomy levels, including miRNA precursor hairpins, hairpin groups and families, mature miRNA loci, mature sequences, and genomic clusters, as well as per-hairpin-position alignment start and base coverage details. -
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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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CallSam
Generic base caller
CallSam reads a sorted bam file and performs base-calling. -
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alnfix
Program to fix issues with helicos bam files.
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Bycom
Bycom can do methylcytosine calling (5mC calling) from BS-seq.
Bycom can do methylcytosine calling from BS-seq (WGBS and RRBS), and either unmapped reads (FASTQ) or mapped reads (SAM/BAM) could be permitted for the input data. Certain SNPs (C>A/G) can also be selected in the output. 1. There's no softwares or methods identify methylcytosines considering the cell heterozygosis caused by multicellular sequencing. Bycom introduced it along with the sequencing errors and unconverson rate based on the Bayesian model. 2. Several parameters in Bycom could be set... -
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VariantMaster
Extract causative variants for monogenic and sporadic genetic diseases
There is a fast growing interest in clinical genetics to the utilization of High Throughput Sequencing data for accurate diagnosis of monogenic diseases. To improve the identification of the variants from HTS, we developed VariantMaster, an original program that accurately and efficiently extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM... -
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Sequence Bias Correction
Sequence bias correction for BAM files without transcript annotations
This sequence bias correction program will take a BAM file of aligned reads and output that file with a correction flag for each read detailing the suggested sequence bias correction weight. It will also produce files for corrected splices and read coverage. -
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Mobster
Mobster: a robust tool for Mobile Element Insertion detection in NGS
Mobster is used to detect novel (non-reference) Mobile Element Insertion (MEI) events in BAM files and uses both a discordant read pair method and a split-read method. -
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a semi... -
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DNase2Hotspots
This software identifies tag-enriched regions(hotspots) from DNase-seq
DNase2Hotspots is a software package for identifying tag-enriched genomic regions (hotspots) from the DNase-Seq genomic data. This program reads a BAM (Binary Alignment/Map) file or tab-delimited text files as input and produces a list of hotspot candidates and associated z-scores as output. Mappability profiles for the reference genome and genomic regions of repeat maskers are also required as input. -
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BriPy
A BRIC-seq data analysis package written in Python.
... analysis. -What is BriPy? BriPy package is a BRIC-seq data analysis tool written in Python. It can calculate RNA half-life for each transcript and draw graphs describing the kinetics of RNA decay. In the future, it will provide several useful modules(e.g. calculating RPKM of each transcript from BAM file or ELAND output file). -Prerequisites To use BriPy package, you will need Python and the following extension packages. Python2.7 or higher NumPy SciPy Matplotlib