| Package Name | Access | Summary | Updated |
|---|---|---|---|
| flash2 | public | Merge paired-end reads from fragments that are shorter than twice the read length | 2025-09-24 |
| squeakr | public | An Exact and Approximate k-mer Counting System. | 2025-09-24 |
| mira | public | MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). | 2025-09-24 |
| perl-sys-info-driver-osx | public | OSX driver for Sys::Info. | 2025-09-24 |
| hyphy | public | An open-source software package for comparative sequence analysis using stochastic evolutionary models. | 2025-09-24 |
| miranda | public | An algorithm for finding genomic targets for microRNAs | 2025-09-24 |
| ariba | public | ARIBA: Antibiotic Resistance Identification By Assembly. | 2025-09-23 |
| ra | public | Ra is short for RNA Assembler and it is a C++ implementation of an overlap-layout-consensus transcriptome assembler. | 2025-09-23 |
| links | public | Long Interval Nucleotide K-mer Scaffolder | 2025-09-23 |
| metilene | public | Fast and sensitive detection of differential DNA methylation | 2025-09-23 |
| gap2seq | public | Gap2Seq is a tool for filling gaps between contigs in genome assemblies. | 2025-09-23 |
| sga | public | SGA - String Graph Assembler. SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads. | 2025-09-23 |
| snpeff | public | Genetic variant annotation and effect prediction toolbox | 2025-09-23 |
| snpsift | public | Toolbox that allows you to filter and manipulate annotated files | 2025-09-23 |
| discosnp | public | reference-free small variant caller for short read sequencing data | 2025-09-23 |
| assembly-stats | public | Get assembly statistics from FASTA and FASTQ files | 2025-09-23 |
| treebest | public | TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline. | 2025-09-23 |
| samtools | public | Tools for dealing with SAM, BAM and CRAM files | 2025-09-23 |
| fastuniq | public | No Summary | 2025-09-23 |
| dsk | public | DSK is a k-mer counter for reads or genomes. | 2025-09-22 |
| r-stitch | public | STITCH - Sequencing To Imputation Through Constructing Haplotypes. | 2025-09-22 |
| fasta3 | public | The FASTA package - protein and DNA sequence similarity searching and alignment programs | 2025-09-22 |
| glimmerhmm | public | No Summary | 2025-09-22 |
| visceral-evaluatesegmentation | public | EvaluateSegmentation is a tool that compares two volumes (a test segmentation and a ground truth segmentation) using 22 different metrics that were selected as a result of a comprehensive research into the metrics used in the medical volume segmentations. | 2025-09-22 |
| survivor | public | Toolset for SV simulation, comparison and filtering | 2025-09-21 |
