Bioinformatics

GenomeTools

GenomeTools is versatile open source genome analysis software.

Genomics General

This is a collection of scripts for a range of genomic data processing and analysis.

GffCompare

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).

Gffread

The program gffread can be used to validate, filter, convert and perform various other operations on GFF files (use gffread -h to see the various usage options).

GSNAP

GSNAP: Genomic Short-read Nucleotide Alignment Program

HISAT2

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 to a single reference genome).

HMMER

Biosequence analysis using profile hidden Markov models.

HTSeq

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

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