NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...uding those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer...uencing error and real genomic variations at the same time and makes i...n of breakpoints stemming from structural variations. The k-mer search...range of different structural variations including nested SVs (e.g. i...2213 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologi...lye performs an extra repeat classification and analysis step to improve the structura...2204 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...for microbial datasets. In real-time mode, it can be integrated with simple structura...2166 days ago
2165 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yi...ts, along with the positions, sequence, and flanking base pairs of each such structura...2186 days ago
2180 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq...plot shows the amount of distinct K-mers absent, as well as the copy number variation present within the assembly....1993 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.2110 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 ca...2110 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection. In such cases rese...2096 days ago