Search Results for "bam-readcount"
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Showing 80 open source projects for "bam-readcount"
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1
mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth is a fast BAM/CRAM depth calculation tool for genomic data, allowing efficient computation of sequencing coverage. -
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rna-test
script for variant calling of RNA-Seq
...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. Mutlithreading for dbsnp annotation, Haplotypecaller, and bamreadcount more efficient. UMI function is added. ... -
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DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. DeepTrio is a deep learning-based trio variant caller built on top of DeepVariant. DeepTrio extends DeepVariant's functionality, allowing it to utilize the power of neural networks to predict genomic variants in trios or duos. ... -
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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. -
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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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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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DirCBMLister
Plugin for TotalCommander to list Commodore disk images
...Currently the following disk image formats are supported: -D64 (1541 images incl. 40 track formats) -D71 (1571 images) -D80 (8050 images) -D81 (1581 images) -D82 (8250 images) Functions: ---------- - view the disk images with the original C64 char set - gives additional info about the disk image like format, D64 40-track type and if error info is available - use it with F3 or Ctrl-Q - shows BAM and error map too - switch between Upper/Graph, Lower/Upper char sets, BAM and error map (if available) with the word wrap key 'w' -
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FastQC
A quality control analysis tool for high throughput sequencing data
...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 then direct you to where your data may have problems and allow you to take necessary steps to correct it before doing any further analysis. FastQC is not tied to any specific type of sequencing technique, so it can be used to look at libraries of various experiment types (Genomic Sequencing, ChIP-Seq, RNA-Seq, BS-Seq etc etc). -
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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 about VARSCAN is corrected. Mutlithreading for dbsnp annotation, Haplotypecaller, Varscan and bamreadcount more efficient. ... -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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svdetectcnv.sh
shell script to run SVDetect with baseline adjustment
...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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Somatic APP analysis
Reanalysis of somatic APP retrotransposition
... [ Basic usage ] • Detection of IEJs connecting APP exons java -jar somaticAPP.jar -D -b input.bam [optional_arguments] * Input data: 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. ... -
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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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miARma-Seq
a A suite designed to study mRNAs, miRNAs and circRNAs
miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together... -
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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 niches. ...
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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. -
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VoltMR
Pure java NGS mapping soft run on Hadoop 2.0
...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 followed after mapping. For RNA mapping, splice aware algorithm is implemented. Volt is open source, released as "LGPLv3" -
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OpenWm
Open webMethods utilities and tools
Open webMethods - some set of utilities and tools (like generic message interceptor based on InvokeManager) to help with integration development, package deployment, debugging, monitoring and maintenance using the farm of Software AG webMethods Integration Servers. There is also an improvement for webMethods Developer 8.2. Not finished yet, with a web UI not published yet. -
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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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wham_bam
Simple script to convert all fastq files in a directory into bam files
The script takes fastq files from sequence runs (or from bam files converted using bam2fastq) and aligns to a user-selected genome. Additional options to only convert reads above a certain mapping score, removing duplicates and generating bed files (requires Bedtools set in path). -
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SeqPig
Use Apache Pig to process your 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
...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
