2179 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...ding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as...2175 days ago
2174 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...osmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X Genomics Linked-Reads proximity-ligation (Hi-C) reads high-coverage sequencing (>40x coverage-per-SNP) using above technolo...2195 days ago
WhatsHap: fast and accurate read-based phasing
...ch as TCG → AGAA) Pedigree phasing mode uses reads from related individuals (such as trios) to improve results and to reduce coverage requirements (Garg et al.,&nb...2182 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...ine Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and...2150 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...een two (or three) sequence files or hashes. sect: SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file us...s produced by different NGS reads. profile: Creates a K-mer coverage plot for a single sequence. T...1995 days ago
Indexcov: fast coverage quality control for whole-genome sequencing
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, an...2089 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and gener...2112 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the developme...2098 days ago