VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To s...e efficient to store only those read-pairs or reads who intersect some region aro...e aspect of the data (e.g. breakpoints), many reads c...2097 days ago
2096 days ago
2096 days ago
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 adapt...n, resulting in high-quality consensus sequences of reads s...2082 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. T...imilarity is defined by comparing the 2nd reads o...2082 days ago
Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads w...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 is used to...ve the results of existing assemblies that are obtained based on short or long sequencing reads.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-t...hput sequencing data. By using local realignment of reads and local assembly it achieve...d high specificity. Platypus can detect SNPs, MNPs, short i...2076 days ago
QUAST-LG: Versatile genome assembly evaluation
QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant q..., we introduce a concept of upper bound assembly for a given genome and set of reads,...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