Search Results for "next-generation dna sequencing"
Sort By:
Showing 36 open source projects for "next-generation dna sequencing"
View related business solutions-
Gen AI apps are built with MongoDB AtlasMongoDB Atlas is the developer-friendly database used to build, scale, and run gen AI and LLM-powered apps—without needing a separate vector database. Atlas offers built-in vector search, global availability across 115+ regions, and flexible document modeling. Start building AI apps faster, all in one place.
-
Yeastar: Business Phone System and Unified CommunicationsUser-friendly, optimized, and scalable, the Yeastar P-Series Phone System redefines business connectivity by bringing together calling, meetings, omnichannel messaging, and integrations in one simple platform—removing the limitations of distance, platforms, and systems.
-
1
FullSSR
SSR detection and primer designing software
Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step. -
2
Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
-
3
miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
miRDeep-P2 (miRDP2) is developed to accurately and fast analyze microRNAs (miRNAs) transcriptome in plants. It is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA... -
4
MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
ServiceDesk Plus, a world-class IT and enterprise service management platformBest in class online service desk software. Offer your customers world-class services with ServiceDesk Plus Cloud, the easy-to-use SaaS service desk software from ManageEngine, the IT management division of Zoho. Track and manage IT tickets efficiently, resolve issues faster, and ensure end-user satisfaction with the cloud-based IT ticketing system used by over 100,000 IT service desks worldwide. Manage the complete life cycle of IT incidents, problems, changes, and projects with out of the box ITIL workflows. Create support SLAs, define escalation levels, and ensure compliance. Automate ticket dispatch, categorization, classification, and assignment based on predefined business rules, and set up notifications and alerts for timely ticket resolution. Reduce walk ins and unnecessary tickets by giving your users more control. Enable end users to access IT services through your service catalog in the self-service portal. Help users create and track tickets and search for solutions.
-
5
GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. ... -
6
bspipe
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq. -
7
...This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/
-
8
CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
...CSBB is currently available on Linux, UNIX. Currently CSBB provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. Providing User with End to End pipeline experience. -
9
The increasing demand of next-generation sequencing (NGS) studies has remarked the necessity of integrated and reliable pipelines to analyse deep-sequencing experiments in an efficient way. We present RUbioSeq+, a stand-alone and multiplatform application for the integrated analysis of NGS data. More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform these common tasks. ...
-
Information Security Made Simple and Affordable | CarbideGet expert guidance and smart tools to launch or level up your security and compliance efforts without the complexity.
-
10
ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
VFS was fullly tested under Ubuntu/Debian system. ** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base... -
11
Meta Assembler for de novo assembly results. GARM (Genome Assembly Reconciliation and Merging) is a pipeline to merge results from different assemblers or results from different DNA sequencing technologies.
-
12
A machine learning-based method for somatic variant identification from low-pass next-generation sequencing.
-
13
BamBam
Tools for genomic analysis
BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball. -
14
NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
The NGS TOOLBOX is a collection of simple open source Perl scripts that perform basic analyses and processing steps using next generation sequencing (NGS) datasets. Each tool is designed to ensure convenient and intuitive usage. Installation and usage does not require any bioinformatics skills. All scripts work out-of-the-box. Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. If you use the NGS TOOLBOX you for publication purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. ... -
15
Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
-
16
AMOS
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. -
17
basecv
BCV is DNA base caller with vocabulary
The Base Calling with Vocabulary (BCV) software package is intended for analysis of direct (population) sequencing chromatograms using known vocabulary sequences similar to the target DNA. The current version of BCV can only process chromatogram files obtained on Applied Biosystems capillary sequencing machines (ABIF file format). -
18
EXCAVATOR-tool
Tool for detecting CNVs from whole-exome sequencing data
ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!! We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR is a novel software package for the detection of copy number variants (CNVs) from whole-exome... -
19
CSEA
Correcting Structural Errors After Genome Assembly
CSEA is a suite of programs for correcting structural errors after assembly without reference, improve the quality of genome assembly. The program is specially designed for second-generation sequencing reads. It also can do denovo assembly and correct errors. Contact: jbtangcn@gmail.com -
20
MspJI-seq_pipeline1.0
an pipeline for MspJI-digesting sequencing in DNA methylation study
MspJI-seq_pipeline1.0 is pipeline for MspJI-digesting sequencing in DNA methylation study. Modification-dependent restriction endonuclease MspJI digestion coupled with next generation sequencing could estimate the methylation state of "CNNR" Cytosine location in the genome by mapping high throughput reads to the reference sequences. MspJI-seq_pipeline1.0 is designed to be a general-purpose mapping program to handle these special characteristics of MspJI-seq. ... -
21
Pop-seq
Population simulator to solve next generation sequencing questions
Pop-seq is a perl based simulation tool, for generating any kind of mapping population using an user defined recombination landscapes. Combined with the Seq-sim tool you can generate pooled or bar-coded next generation sequencing biased outcomes. This tool were used to solve reappearing question in a experimental design (e. g. of how many plants or sequencing depth is advisable in a back crossed or out crossed scenario ) -
22
TANGO is one of the most accurate tools for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy
-
23
T-lex
Transposable Element annotation using Next-Generation Sequencing data
The T-lex package contains two pipelines. The T-lex pipeline calls presence/absence of known TE insertions using re-sequencing data. On top of the genotyping, this pipeline also allows to re-annotate TEs and discover traces of transposition events called Target Site Duplication (TSD). The other T-lex pipeline discovers and annotates de novo TE insertions. http://petrov.stanford.edu/cgi-bin/Tlex.html -
24
TaxoAssignement
Taxonomic assignement of sequences
TANGO is one of the most accurate tools for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy -
25
BreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.