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
2299 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
2221 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
2068 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
2004 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
1946 days ago
Tags: Cogent, tool, reconstruct, coding, genome, high-quality, full-length, transcriptome, sequences, genome, evaluation
1768 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
747 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
2935 days ago
Tags: Bioinformatics, FASTQ, NGS, ALE, Framework, Stats, Reads, Evaluation, Quality, Assembly
2916 days ago
gEVAL: Genome Evaluation Browser
The gEVAL Browser allows the evaluation of genome assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assist in strategizing potential solutions for these issues. Th...Tags: gEVAL, Genome, Evaluation, Browser
1768 days ago