Results for "analysis"

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  • ScaffMatch

    caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one needs to first map reads to contigs (instead of...

    Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, ScaffMatch, Scaffoldings

    2663 days ago

  • BIMA V3: an aligner customized for mate pair library sequencing

    Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a challenging and time consuming process for most NGS alig...

    Tags: Bioinformatics, Analysis, Genome, Mapping, NGS, BIMA, Reads

    2662 days ago

  • E-MEM: Efficient computation of Maximal Exact Matches

    E-MEM is a C++/OpenMP program designed to efficiently compute MEMs between large genomes. See the README file for instructions on how to use E-MEM. E-MEM source code The source code can be downloaded here. If you use E-MEM, please cite: N. Khiste, L. Ilie, E-MEM: Efficient comp...

    Tags: Bioinformatics, Analysis, Match, Genome, E-MEM

    2661 days ago

  • Gene Synteny Database

    Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to i...

    Tags: Bioinformatics, Analysis, Synteny, Database, Genomicus

    2660 days ago

  • GARM:Genome Assembly, Reconciliation and Merging

    The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaf...

    Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, Merge, GARM

    2657 days ago

  • GAM-NGS: genomic assemblies merger for next generation sequencing

    GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus ...

    Tags: Bioinformatics, Analysis, Assembly, Genome, GAM-NGS

    2657 days ago

  • PEAR

    PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it ...

    Tags: Bioinformatics, Analysis, Assembly, Genome, PEAR, Merge, Paired-End

    2657 days ago

  • MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs

    MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs) Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any length in Multi-FASTA format to produce an improved c...

    Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, Merge, MeGAMerge

    2657 days ago

  • quickmerge: A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

    quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBi...

    Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, QuickMerge

    2657 days ago

  • Genome Assembly Tutorial

    If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard to assemble using overlap-consensus-layout appr...

    Tags: Bioinformatics, Analysis, Assembly, Genome, De Bruijn graph

    2656 days ago