nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifi...1935 days ago
geck: trio-based comparative benchmarking of variant calls
...Caller on the high-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome trios. We show that our method is able to estimate differential precis...1826 days ago
GffCompare: Program for processing GTF/GFF files
The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).1776 days ago
ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
...whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from the data). By...1584 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...lt: false) -maxcorK INT: the maximum number of correction within k-bp window (default: 4) -wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lo...1565 days ago
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
...sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA seque...1270 days ago