Search Results for "illumina"
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Showing 54 open source projects for "illumina"
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BBMap
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity... -
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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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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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methylr
a single shiny solution from sequencer data to pathway analysis
Here we introduce methylR, a complete pipeline for the analysis of both 450K and EPIC Illumina arrays which not only offers data visualization and normalization but also provide additional features such as the annotation of the genomic features resulting from the analysis, pairwise comparisons of DMCs with different graphical representation plus functional and pathway enrichment as downstream analysis, all packed in a minimal, elegant and intuitive graphical user interface which brings... -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee... -
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SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether...
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub... -
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HaploMiner
A tool to construct haplotypes in diploid species
Download MFbio.jar from Files section. To run the pipeline please refer to Wiki page https://sourceforge.net/p/haplotypeminer/wiki/Documentation/ -
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altanalyze
Alternative splicing and functional prediction analysis tool
... as many conventional array-types (e.g., Affymetrix, Illumina, Agilent). This software requires no advanced knowledge of bioinformatics programs or scripting. All you will need are your junction/exon read or microarray files along with some simple descriptions of the conditions that you're analyzing. RNASeq support is introduced in AltAnalyze 2.0. AltAnalyze documentation, installers are provided on this website as well as at http://www.altanalyze.org. For questions not addressed here, please co -
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novoBreak
Robust detection of somatic structural breakpoints in cancer genomes
.... It was designed for Illumina paired-end data. -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting... -
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ngopt
de novo assembly & analysis of Illumina sequence data
de novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system -
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MT-Toolbox
Software for molecule tagged DNA sequences
MT-Toolbox is a user friendly software package for analysis of molecule tagged Illumina MiSeq reads. Molecule tagging is a molecular biology technique to significantly reduce amplicon sequence error and PCR bias which can be applied to any amplicon sequencing project. MT-Toolbox converts raw reads into high quality consensus sequences based on each reads molecule tag. For details and other important information please refer to the MT-Toolbox webpage below. MT-Toolbox is now hosted... -
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GNomEx
A Genomic LIMS and Data Repository
Our source code is now on GitHub: https://github.com/hci-gnomex/gnomex. Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing, Affy... -
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MuffinEC
Multi-technology, INDEL aware error correction for NGS data
MuffinEC is an error correction software capable of handling all types of errors (insertion deletions, mismatches and unknown bases). It officially supports four technologies (Illumina, 454, ion Torrent and PacBio - experimental) and it also has a generic setup for others (old and/or new). It is released under LGPL version 3.0. MuffinEC can use multicore systems, thanks to its OpenMP implementation. We are developing the 2nd version of MuffinEC. The beta version is already available online... -
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MutAid
MutAid: Sanger and NGS based pipeline for mutation screening.
... 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... -
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.... Visit http://www.biomedcentral.com/1471-2164/15/858/abstract for the pdf article describing the utility of iMSAT and if you use the program please cite this article as: Andersen and Mills: iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries. BMC Genomics 2014 15:858.
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pyQPCR is a GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu
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HBS-tools
a set of tools for hairpin bisulfite-seq data analysis
The emerging genome-wide hairpin bisulfite sequencing technique facilitates the determination of DNA methylation fidelity and accurate methylation calling. Here we present HBS analyzer, the first command line based open-source tool to process genome-wide hairpin bisulfite sequencing data. It accepts Illumina paired-end sequencing reads as input, performs alignment to recover the original (pre-bisulfite-converted) DNA sequences and calls methylation status for cytosines on both DNA strands. -
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The Genome Mappability Analysis suite is used for measuring how well NGS reads can be mapped to reference genomes, especially for discovering variations
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3Dec
Accurate base caller for Illumina non-pattern sequencing platform
Accurate base caller for Illumina non-pattern sequencing platform -
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bsclient
An interactive FTP-like command-line BaseSpace download client
bsclient is an interactive text-based client for browsing and downloading files from Illumina BaseSpace. It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient -
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bisReadMapper
Software for dealing with DNA methylation sequencing data
Fast and lightweight package for analysis of bisulfite converted DNA sequencing reads from the Illumina sequencing platform. -
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EnsembleAssembly
Ensemble de novo sequence assembly of metagenomic data
EnsembleAssembler performs de novo assembly of pathogen genomes from metagenomic samples sequenced using Illumina platforms. EnsembleAssembler optimizes contig formation by integrating results from multiple assemblers including SOAPDenovo2, ABySS, MetaVelvet, and Cap3. The software does NOT perform preprocessing. The user needs to do preprocessing with other software before attempting for assembly. -
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AFSM_seq
a simple and rapid method for genome-wide SNP and methylation site
Reference based analysis 1.Filter the raw reads obtained from Illumina Raw Data (paired-ends)according to your desired stringency, to produce a set of high-quality (HQ) sequences in fastq format. 2.Lignment reads (HQ, Fastq format) against Barcode file (Fasta format) using scanAP program. 3.Trim barcodes and filter paired-ends using trim_seq.pl. Classified paired-ends using fltfastq2pe.pl. to produce output “R1.trim.pair.fastq” and “R2.trim.pair.fastq”. 4.The filtered sequence reads were...