2534 days ago
2532 days ago
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
...strained binary quadratic programming approximation of the original problem. We compared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes. O...2531 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
...be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.2530 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
...tive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/...h, anchored). Overlapping of reads for de novo assembly. &n...e novo assemblies from raw nanopore and PacBio reads without requiring error corre...2516 days ago
Omega2: metagenome assembly pipeline
Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming...ates Omega can more efficiently assemble longer Illumina reads, and at deeper coverage, for...2483 days ago
2483 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
...whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabas...contigs are ordered and oriented using paired reads separated by ∼280 bp or &...2363 days ago
QuorUM: An Error Corrector for Illumina Reads
...relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low...mber of low-count erroneous k-mers in the reads. However, there is enough inf...M is mainly aimed at error correcting Illumina reads for subsequent assembly. It i...2362 days ago
Unicycler: Hybrid assembly pipeline for bacterial genomes
...acBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid...2360 days ago