Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use...1702 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be...1690 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. It...ph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be...1640 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 Windows1629 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 whole-g...nCNV). Of course it is better if your samples were sequenced within the same sequencing facility.1629 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...1629 days ago
1620 days ago
Genome in a Bottle (GIAB) Consortium
The Genome in a Bottle (GIAB) Consortium is a public-private-academic consortium hoste...nce methods, and reference data) to enable translation of whole human genome sequencing to clinical practice. https...1620 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...n human genome, counts the frequency of k-mers in sequencing data and predicts the genotyp...1617 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/vt1617 days ago