| Package Name | Access | Summary | Updated |
|---|---|---|---|
| hivmmer | public | An alignment and variant-calling pipeline for Illumina deep sequencing of HIV-1, based on the probabilistic aligner HMMER. | 2025-03-25 |
| bowtie2 | public | Fast and sensitive read alignment | 2025-03-25 |
| tbb | public | Intel(R) Threading Building Blocks (Intel TBB) | 2025-03-25 |
| mafft | public | Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform | 2025-03-25 |
| xgboost | public | eXtreme Gradient Boosting | 2025-03-25 |
| blast | public | BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit | 2025-03-25 |
| ampliconclipper | public | an alignment postprocessor that removes PCR primers from SAM alignments and discards reads with major errors | 2025-03-25 |
| sra-tools | public | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | 2025-03-25 |
| picard | public | Java tools for working with NGS data in the BAM format | 2025-03-25 |
| trimmomatic | public | A flexible read trimming tool for Illumina NGS data | 2025-03-25 |
| iva | public | de novo virus assembler of Illumina paired reads | 2025-03-25 |
| mummer | public | MUMmer is a system for rapidly aligning entire genomes | 2025-03-25 |
| biomake | public | GNU-Make-like utility for managing builds and complex workflows | 2025-03-25 |
| swi-prolog | public | A comprehensive Prolog implementation | 2025-03-25 |
| kmc | public | Fast and frugal disk based k-mer counter | 2025-03-25 |
| fastaq | public | Python3 scripts to manipulate FASTA and FASTQ files | 2025-03-25 |
| pysam | public | Python module for reading and manipulating SAM/BAM/VCF/BCF files | 2025-03-25 |
| samtools | public | Tools for dealing with SAM, BAM and CRAM files | 2025-03-25 |
| smalt | public | SMALT aligns DNA sequencing reads with a reference genome. | 2025-03-25 |
| bambamc | public | lightweight C implementation of name collating BAM file input and BAM file output | 2025-03-25 |
| prinseq | public | PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data | 2025-03-25 |
| fastx_toolkit | public | FASTA/FASTQ pre-processing programs | 2025-03-25 |
| libgtextutils | public | Gordon's Text utils Library | 2025-03-25 |
| hmmer | public | Biosequence analysis using profile hidden Markov models | 2025-03-25 |
| pear | public | PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger | 2025-03-25 |
