LoRMA: A tool for correcting sequencing errors in long reads
...ts. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 7...2088 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
...n the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, r...2045 days ago
QUAST-LG: Versatile genome assembly evaluation
...equences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a conce...2039 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
...y exploring a number of possible solutions which is exponential in the coverage of the dataset. The parallel...high accuracy as that provided by WhatsHap, which increases with coverage. https://bmcbioinformatics...2019 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
...ts an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a...1991 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...move one of them to the haplotig 'pool'. The pipeline uses mapped read coverage and Minimap2 alignments to de...tionally produced for all flagged contig matches, juxtaposed with read-coverage, to help the user determine t...1987 days ago
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mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
...ed at or above a given threshold for each chromosome and genome-wide.quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)threshold ou...1652 days ago
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
...test data are publicly accessible at the project documentation site http://biodatageeks.org/sequila/benchmarking/benchmarking.html#depth-of-coverage. An archival copy of the code...1623 days ago