Circlator: automated circularization of genome assemblies using long sequencing reads
...rithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al...2239 days ago
2231 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2230 days ago
WhatsHap: fast and accurate read-based phasing
...ftware for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well wi...2226 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BM...2208 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...it clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference..../minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads ./minimap2 -ax splice...2203 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...sassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the init...to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differen...2187 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/nanofilt2162 days ago
REVIGO: Reduced Visualize gene ontology
REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatter...2162 days ago
LSC :a long read error correction tool
...is unclear. You're ready, Happy LSCing! Latest publication Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong Improving PacBio Long Read Accuracy by Short Read A...2160 days ago