FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.2618 days ago
2616 days ago
Pacbio Long Reads Compatible Software and Tools
...A separate page lists commercial software. Know of any other open source software for PacBio data? Email us. Software categories: De novo assembly Structural Variatio...2601 days ago
ChromHMM: Chromatin state discovery and characterization
...terizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combina...2567 days ago
A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
...o generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely re...2544 days ago
SuRankCo: supervised ranking of contigs in de novo assemblies
SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known re...2532 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
...ctor and Gotoh, anchored). Overlapping of reads for de novo assembly. T...bsp; ...and much more.GraphMap is also used as an overlapper in a new de novo genome assembly project calle...2518 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina r...2365 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly...2345 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...rror). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly conti...2343 days ago