| Package Name | Access | Summary | Updated |
|---|---|---|---|
| alfred | public | BAM alignment statistics, feature counting and feature annotation | 2025-08-22 |
| skesa | public | Strategic Kmer Extension for Scrupulous Assemblies & Sequence Assembly Using Target Enrichment | 2025-08-21 |
| bioconductor-chromvar | public | Chromatin Variation Across Regions. | 2025-08-21 |
| macs2 | public | Model Based Analysis for ChIP-Seq data | 2025-08-21 |
| btrim | public | This tool is made to remove "tips" (short dead ends) from a compacted de Bruijn graph and more generally to remove sequencing errors. Used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336) | 2025-08-21 |
| disco | public | Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler. | 2025-08-21 |
| sparseassembler | public | No Summary | 2025-08-21 |
| dbg2olc | public | Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies | 2025-08-21 |
| assemblyutility | public | No Summary | 2025-08-21 |
| sparc | public | No Summary | 2025-08-21 |
| perl-findbin | public | Locate directory of original perl script. | 2025-08-20 |
| augustus | public | AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. | 2025-08-20 |
| perl-bio-phylo | public | An object-oriented Perl toolkit for analyzing and manipulating phyloinformatic data. | 2025-08-20 |
| perl-bio-db-hts | public | Read files using HTSlib including BAM/CRAM, Tabix and BCF database files | 2025-08-20 |
| paml | public | A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | 2025-08-20 |
| bioconductor-dupradar | public | Assessment of duplication rates in RNA-Seq datasets | 2025-08-20 |
| ushuffle | public | uShuffle---a useful tool for shuffling biological sequences while preserving the k-let counts | 2025-08-20 |
| samblaster | public | Mark duplicates in and extract discordant and split reads from SAM files. | 2025-08-19 |
| perl-inline-c | public | C Language Support for Inline. | 2025-08-19 |
| dxpy | public | DNAnexus Platform API bindings for Python | 2025-08-19 |
| nanoplot | public | Plotting suite for long read sequencing data and alignments. | 2025-08-19 |
| fastq-tools | public | A collection of fastq manipulation scripts written in C for speed. | 2025-08-19 |
| seqkit | public | A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. | 2025-08-19 |
| r-aroma.affymetrix | public | A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006. | 2025-08-19 |
| pbsim | public | No Summary | 2025-08-19 |
