scoreseq

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SCORE-Seq is a command-line program which implements score statistics for detecting disease associations with rare variants in sequencing studies.

rdptools

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The RDPTools project includes the modules from the RDP (Classifier, Clustering, SequenceMatch, ProbeMatch, InitialProcessing, FrameBot, ReadSeq, Xander) and all their dependencies.

mass

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MASS is a command-line program written in C to perform fixed-effects (FE) and random-effects (RE) meta-analysis of sequencing studies by combining the score statistics from multiple studies.

hisat2

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HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome).

impute

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IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program’s basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.

gffcompare

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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).