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-gene...t to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if...2038 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 of reads and local assembly it achieves bo...2017 days ago
vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once...2017 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
...Quire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases ar...1919 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...hole pipeline with SV calling takes ~2 minutes. Intact ordering and orienting of contigs. Chimeric contig correction GFF lift-over Structural variant calling with and integrated v...1843 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkena...1811 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1744 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) read...genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and...1744 days ago
1686 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...he whole pipeline with SV calling takes ~2 minutes. Intact ordering and orienting of contigs. Misassembly correction GFF lift-over Structural variant calling with and integrated v...1651 days ago