Stars
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Tools (written in C using htslib) for manipulating next-generation sequencing data
bedtools - the swiss army knife for genome arithmetic
De novo assembler for single molecule sequencing reads using repeat graphs
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
Tandem Repeats Finder: a program to analyze DNA sequences
Find all significant local alignments between reads
Integrated toolkit for analysis and evaluation of annotated genomes
mdust from DFCI Gene Indices Software Tools (archived for a historical record only)
semi-automatic classification and postprocessing of LTR retrotransposons