Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-08...Tags: Circlator, automated, circularization, genome, assemblies, sequencing, reads
2192 days ago
Tags: Mapping, single, molecule, sequencing, reads, Basic, Local, Alignment, Successive, Refinement, BLASR
2185 days ago
Tags: Manta, rapid, detection, structural, variants, indels, germline, cancer, sequencing, applications
2179 days ago
Tags: BFC, standalone, high-performance, tool, correcting, sequencing, errors, Illumina, sequencing, data
2176 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmi...Tags: npScarf, real-time, scaffolder, SPAdes, contigs, Nanopore, sequencing, reads
2166 days ago
Tags: ChopStitch, exon, annotation, splice, graph, transcriptome, assembly, whole, genome, sequencing
2144 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofiltTags: nanofilt, filter, trim, long, read, sequencing, NGS, nanopore
2116 days ago
gSearch: a fast and flexible general search tool for whole-genome sequencing
gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.Tags: gSearch, fast, flexible, search, tool, whole-genome, sequencing
2109 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 generates two integrated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV is in AN...Tags: NextSV, meta-caller, structural, variants, low-coverage, long-read, sequencing, data
2109 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number...Tags: PureCN, copy, number, calling, SNV, classification, targeted, short, read, sequencing
2107 days ago