StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo&nbs...1482 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS long reads....raph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be...1638 days ago
ngs-bits - Short-read sequencing tools
Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows1626 days ago
ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and who...linCNV). Of course it is better if your samples were sequenced within the same sequencing facility.1626 days ago
MGSE: Mapping-based Genome Size Estimation
MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all avai...1626 days ago
1618 days ago
Genome in a Bottle (GIAB) Consortium
The Genome in a Bottle (GIAB) Consortium is a public-private-academic consortium h...rence methods, and reference data) to enable translation of whole human genome sequencing to clinical practice. https...1618 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and...in human genome, counts the frequency of k-mers in sequencing data and predicts the genotyp...1615 days ago
vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt1615 days ago
HASLR: a tool for rapid genome assembly of long sequencing reads
HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which mean...long reads generated by Third Generation Sequencing technologies (such as PacBio...Nanopore) together with Next Generation Sequencing reads (such as Illumina) from...1612 days ago