| Package Name | Access | Summary | Updated |
|---|---|---|---|
| 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 |
| expansionhunter | public | A tool for estimating repeat sizes | 2025-09-21 |
| vt | public | A tool set for short variant discovery in genetic sequence data | 2025-09-21 |
| concoct | public | Clustering cONtigs with COverage and ComposiTion | 2025-09-20 |
| samsift | public | Advanced filtering and tagging of SAM/BAM alignments using Python expressions. | 2025-09-19 |
| ngs-disambiguate | public | Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem | 2025-09-19 |
| snp-dists | public | Convert a FASTA alignment to SNP distance matrix | 2025-09-19 |
| smalt | public | SMALT aligns DNA sequencing reads with a reference genome. | 2025-09-18 |
| edena | public | No Summary | 2025-09-18 |
| rust-bio-tools | public | A growing collection of fast and secure command line utilities for dealing with NGS data implemented on top of Rust-Bio. | 2025-09-18 |
| abyss | public | Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler. | 2025-09-18 |
