Results for "evaluation"

Tags

  • #Scaffolder #evaluation with #Python #scripts https://github.com/martinghunt/Scaffolder-evaluation/tree/master/Analysis-scripts

    Tags: Scaffolder, evaluation, Python, scripts

    2971 days ago

  • Seal: SEquence ALignment evaluation suite

    Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference genome from one or more FASTA files. Alternativ...

    Tags: Seal, SEquence, ALignment, evaluation, suite

    2276 days ago

  • repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric

    Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two contigs A and B is considered correct if: Their relative orientation is correct Their relative order is correct The gap estimate...

    Tags: Repeat, aware, scaffolding, evaluation, framework, Igor, Mandric, repeat-aware

    2199 days ago

  • LRCstats: a tool for evaluating long reads correction methods

    LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are lon...

    Tags: LRCstats, tool, evaluation, long, reads, correction, methods

    2045 days ago

  • QUAST-LG: Versatile genome assembly evaluation

    QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for ...

    Tags: QUAST-LG, Versatile, genome, assembly, evaluation

    1981 days ago

  • Versatile genome assembly evaluation with QUAST-LG

    QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST  package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large ...

    Tags: Versatile, genome, assembly, evaluation, QUAST-LG

    1924 days ago

  • Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.

    Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.   Cogent is a tool for reconstruct...

    Tags: Cogent, tool, reconstruct, coding, genome, high-quality, full-length, transcriptome, sequences, genome, evaluation

    1745 days ago

  • Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

    Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s interna...

    Tags: Merfin, improved, variant, filtering, assembly, evaluation, polishing, k-mer, validation

    725 days ago

  • REAPR: a universal tool for genome assembly evaluation

    REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual insp...

    Tags: Bioinformatics, Computational Biology, Assembly, Comparison, Accuracy, Evaluation

    2913 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