BASE: a practical de novo assembler for large genomes using long NGS reads
new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high p...2082 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC i...r improve the results of existing assemblies that are obtained based on short or long sequencing...2076 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment...sand Genomes and WGS500 projects, and is being used in clinical sequencing...2076 days ago
COSINE: non-seeding method for mapping long noisy sequences
Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.2075 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process...2065 days ago
AMStat: display statistics of large sequence files from next generation sequencing projects
SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmappe...2060 days ago
Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: ht...2058 days ago
sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
Required python modules biopython intervaltree numpy scipy tqdm PyYAML2057 days ago
2056 days ago
Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep co...epbinner is more computationally intensive than Porechop. You used a sequencing...2043 days ago