Results for "NGS"

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  • DISCOVAR

    DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or longer — produced on MiSeq or HiSeq 2500 &m...

    Tags: Bioinformatics, NGS, Assembly, DISCOVAR, Variants, BroadInstitute

    2901 days ago

  • SPAdes

    SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau...

    Tags: Bioinformatics, NGS, Assembly, Assembler, SPAdes, Reads, Illumina

    2900 days ago

  • BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

    High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures like N50.  BUSCO provides measures for q...

    Tags: Bioinformatics, Validation, Assembly, BUSCO, Orthologs, NGS

    2879 days ago

  • segemehl

    segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation conta...

    Tags: Bioinformatics, FASTQ, Reads, Map, Mapping, Segemehl, NGS

    2879 days ago

  • ALE: a Generic Assembly Likelihood Evaluation Framework for Assessing the Accuracy of Genome and Metagenome Assemblies

    Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and inse...

    Tags: Bioinformatics, FASTQ, NGS, ALE, Framework, Stats, Reads, Evaluation, Quality, Assembly

    2893 days ago

  • HOMER: Software for motif discovery and next-gen sequencing analysis

    This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER. Setting up your computing environment Retrieving and storing sequencing files (your own data or from public so...

    Tags: Bioinformatics, NGS, Motif, Tutorial

    2893 days ago

  • mrFAST: Micro Read Fast Alignment Search Tool

    mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes ...

    Tags: Bioinformatics, FASTQ, Reads, NGS, Mapping, Alignment, Reference

    2893 days ago

  • CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.

    Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is a hierachical assembly pipeline which runs in fo...

    Tags: Bioinformatics, FASTQ, NGS, Assembly, Genome, CANU, Assembler, Tool, Software

    2876 days ago

  • MEDEA: Comparative Genomic Visualization with Adobe Flash

    As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets. More at http:/...

    Tags: Bioinformatics, NGS, Visualization, Chromosome, Comparative genomics

    2893 days ago

  • Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

    Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ...

    Tags: Bioinformatics, Visualization, Alignment, Free, NGS, Comparative Genomics

    2893 days ago