Search Results for "sanger"
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Showing 21 open source projects for "sanger"
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Gemi
PCR primers / probes design from multiple & degenerate sequences
...Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. Python codes can be supported upon request. Article: Gemi: PCR primers prediction from multiple alignments Comparative and functional genomics 2012;2012:783138 DOI: https://doi.org/10.1155/2012/783138 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117 PMCID: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535827/ -
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XLibraryDisplay
A sequence analysis tool for protein engineering
...It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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...The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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Pipebar
A fast and accurate pipeline for DNA barcoding analysis.
Molecular analyses require the use of multiple bioinformatics tools. Here we proposed a pipeline for DNA chromatograms analysis of Sanger platform by open-source tools integration in order to reduce cost with standard commercial licences ensuring high quality, robustness with reduced time. Pipebar is a python application created to automatization of processing chromatogram trace files to high-quality DNA sequences for downstream analyses. -
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BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
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DaMold
a data mining platform for variant annotation and visualization.
DaMold a powerful, integrated, web-based, and user-friendly tool to filter, annotate, cross-link, and visualize NGS, Sanger, and hotspot variants. It is easy-to-use software, which provides flexible input options and accepts variants in VCF and BED formats. For each variant DaMold predicts the variant effect, such as codon change, and amino acid change. Furthermore, it cross-links each variant with more than 30 clinically relevant public databases, which contain already reported SNPs and INDELs from previous experimental studies along with associated genomic, proteomic, and clinical information. ... -
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MutAid
MutAid: Sanger and NGS based pipeline for mutation screening.
MutAid: Sanger and NGS based integrated pipeline for mutation identification, validation and annotation in molecular diagnosis. MutAid is an integrated pipeline for mutation screening in clinical research. It can analyze Sanger sequencing and NGS data from raw reads to list of annotated mutation list. MutAid can analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. -
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GNomEx
A 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 and Agilent Microarrays, Sequenom MassArray and Bioanalyzer. GNomEx is a web application with a Flash client user interface and a Java backend that runs on Apache Tomcat. MySQL is used for the database, although any modern RDBMS can be used. -
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ClinQC
ClinQC: A tool for quality control of Sanger and NGS data in clinic
ClinQC is an integrated and user-friendly pipeline for quality control, filtering and trimming of Sanger and NGS sequencing data for hundred to thousands of samples/patients in a single run in clinical research. It can analyze raw sequencing data and produces unified output as FASTQ files per sample/patient with Sanger quality encoding. First, ClinQC convert input read files from their native formats to a common FASTQ format and remove adapters, and PCR primers. -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
...Using finished clones for QC, the pipeline is able to obtain assemblies with clone coverage of 99.7% and consensus base quality of Q39. Developed at the Wellcome Trust Sanger Institute. -
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ArtificialFastqGenerator
Ouputs artificial FASTQ files derived from a reference genome.
ArtificialFastqGenerator takes the reference genome (in FASTA format) as input and outputs artificial FASTQ files in the Sanger format. It can accept Phred base quality scores from existing FASTQ files, and use them to simulate sequencing errors. Since the artificial FASTQs are derived from the reference genome, the reference genome provides a gold-standard for calling variants (Single Nucleotide Polymorphisms (SNPs) and insertions and deletions (indels)). -
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PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/MutationMapper) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/MutationMapper/releases/latest). Predict functional consequences of mutations identified from sanger sequencing.
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The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms
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SOAPsnp
Soapsnp in house version, multi-thread and bam format supported.
...In the first Asian genome re-sequencing project, evalution of SOAPsnp result on Illumina HapMap 1M BeadChip Duo genotyping sites shows great accuracy. Over 99% of the genotyping sites are covered at over 99.9% consistency. Further PCR plus Sanger sequencing of the inconsistent SNP sites confirmed majority of the SOAPsnp results. -
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fastqz
FASTQ file compressor
fastqz is a compressor for the most common (Sanger format) FASTQ files produced by DNA sequencing machines. It may be used with a reference genome for better compression. -
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Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. Suitable for mammalian repertoire sequences obtained either by Sanger or 454 sequencing. Methods published in Glanville, Zhai, Berka et al, PNAS 2009.
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BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.
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The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.
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SeqDoC+
Bioinformatics tool for identifying point mutations in Sanger traces.
SeqDoC+ consists of: seqdoc, a utility based on Mark Crowe's SeqDoC for comparing a pair of Sanger-sequencing DNA traces to identify point mutations; and additional scripts for identifying discrepancies between the raw DNA trace comparison and a BLAST alignment of the corresponding inferred sequences. Positions in the BLAST alignment that are unsupported by SeqDoC may suggest point mutations or base caller errors that would go undetected if one relied solely on the inferred DNA sequences. ...
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