| Package Name | Access | Summary | Updated |
|---|---|---|---|
| novoloci | public | Haplotype-aware assembler for complex regions and small genomes (ONT/HiFi). | 2025-09-23 |
| switchtfi | public | Implementation of the SwitchTFI method as presented in: https://doi.org/10.1101/2025.01.20.633856 | 2025-09-23 |
| cagecleaner | public | Genomic redundancy removal tool for cblaster hit sets. | 2025-09-23 |
| gap2seq | public | Gap2Seq is a tool for filling gaps between contigs in genome assemblies. | 2025-09-23 |
| ltr_finder | public | LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. | 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 |
| altex-be | public | Automatically design sgRNA for exon skipping with many base editors. | 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 |
| funannotate | public | funannotate: eukaryotic genome annotation pipeline | 2025-09-23 |
| discosnp | public | reference-free small variant caller for short read sequencing data | 2025-09-23 |
| cactus | public | Cactus is a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs | 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 |
| mindthegap | public | MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. | 2025-09-23 |
| short-read-connector | public | Short read connector enables the comparisons of two read sets | 2025-09-23 |
| upimapi | public | UniProt Id Mapping through API | 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 |
| generax | public | GeneRax: a parallel tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss. | 2025-09-22 |
| physher | public | A multi-algorithmic framework for phylogenetic inference | 2025-09-22 |
| r-stitch | public | STITCH - Sequencing To Imputation Through Constructing Haplotypes. | 2025-09-22 |
| b2btools | public | The bio2Byte software suite to predict protein biophysical properties | 2025-09-22 |
| fasta3 | public | The FASTA package - protein and DNA sequence similarity searching and alignment programs | 2025-09-22 |
