MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for e...Tags: MECAT, fast mapping, error correction, de novo, assembly, genome, single-molecule, sequencing, reads, Tools
2180 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccura...Tags: HapCUT2, robust, accurate, haplotype, assembly, diverse, sequencing, technologies
2176 days ago
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
2176 days ago
Tags: Mapping, single, molecule, sequencing, reads, Basic, Local, Alignment, Successive, Refinement, BLASR
2168 days ago
Tags: Manta, rapid, detection, structural, variants, indels, germline, cancer, sequencing, applications
2163 days ago
Tags: BFC, standalone, high-performance, tool, correcting, sequencing, errors, Illumina, sequencing, data
2160 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
2149 days ago
Tags: ChopStitch, exon, annotation, splice, graph, transcriptome, assembly, whole, genome, sequencing
2127 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
2100 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
2092 days ago