| Package Name | Access | Summary | Updated |
|---|---|---|---|
| tracy | public | Basecalling, alignment, assembly and deconvolution of Sanger chromatogram trace files | 2025-08-04 |
| rscape | public | R-scape (RNA Structural Covariation Above Phylogenetic Expectation) looks for evidence of a conserved RNA secondary structure by measuring pairwise covariations observed in an input multiple sequence alignment. | 2025-08-04 |
| sickle-trim | public | Windowed Adaptive Trimming for fastq files using quality | 2025-08-04 |
| bifrost | public | Highly parallel construction and indexing of colored and compacted de Bruijn graphs | 2025-08-04 |
| libgff | public | A simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase. | 2025-08-04 |
| slow5tools | public | Toolkit for S/bLOW5 format | 2025-08-04 |
| cooltools | public | Analysis tools for genomic interaction data stored in .cool format | 2025-08-04 |
| unicycler | public | Hybrid assembly pipeline for bacterial genomes | 2025-08-04 |
| yacrd | public | Yet Another Chimeric Read Detector, with long-read mapper result as input. | 2025-08-04 |
| perl-text-balanced | public | Extract delimited text sequences from strings. | 2025-08-04 |
| prophyle | public | ProPhyle is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier. | 2025-08-04 |
| amira | public | A tool to detect acquired AMR genes directly from long read sequencing data. | 2025-08-04 |
| krakentools | public | KrakenTools scripts for analysis of Kraken/KrakenUniq/Kraken2/Bracken results | 2025-08-02 |
| perl-bio-samtools | public | Read SAM/BAM files | 2025-08-01 |
| enabrowsertools | public | enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily. | 2025-08-01 |
| perl-html-tidy | public | (X)HTML validation in a Perl object | 2025-08-01 |
| rtk | public | rtk - rarefaction toolkit for OTU tables | 2025-08-01 |
| ontime | public | Extract subsets of ONT (Nanopore) reads based on time | 2025-08-01 |
| impg | public | impg: implicit pangenome graphs. | 2025-08-01 |
| emblmygff3 | public | An efficient way to convert gff3 annotation files into EMBL format ready to submit. | 2025-08-01 |
| clair3-illumina | public | Clair3 with libraries to support variant calling using Illumina short-reads. Version in sync with Clair3. | 2025-08-01 |
| clair3 | public | Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration. | 2025-08-01 |
| seqfu | public | DNA sequence utilities | 2025-08-01 |
| oligomap | public | Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases. | 2025-08-01 |
| stereogene | public | StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data | 2025-08-01 |
