hivmmer
by hivmmer (Organization)
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| ampliconclipper | 0.0 | an alignment postprocessor that removes PCR primers from SAM alignments and discards reads with major errors | Mar 25, 2025 | GPLv3 |
| bambamc | 0.0.50 | lightweight C implementation of name collating BAM file input and BAM file output | Mar 25, 2025 | GPLv3 |
| biomake | 0.1.3 | GNU-Make-like utility for managing builds and complex workflows | Mar 25, 2025 | BSD |
| blast | 2.7.1 | BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit | Mar 25, 2025 | Public Domain |
| bowtie2 | 2.3.4.1 | Fast and sensitive read alignment | Mar 25, 2025 | GPLv3 |
| bzip2 | 1.0.6 | high-quality data compressor | Mar 25, 2025 | BSD |
| fastaq | 3.15.0 | Python3 scripts to manipulate FASTA and FASTQ files | Mar 25, 2025 | GPLv3 |
| fastx_toolkit | 0.0.14 | FASTA/FASTQ pre-processing programs | Mar 25, 2025 | AGPL |
| hivmmer | 0.1.0 | An alignment and variant-calling pipeline for Illumina deep sequencing of HIV-1, based on the probabilistic aligner HMMER. | Mar 25, 2025 | BSD-like |
| hmmer | 3.1b2 | Biosequence analysis using profile hidden Markov models | Mar 25, 2025 | GPLv3 |
| iva | 1.0.8 | de novo virus assembler of Illumina paired reads | Mar 25, 2025 | GPLv3 |
| kmc | 3.0.0 | Fast and frugal disk based k-mer counter | Mar 25, 2025 | GPLv2 |
| libgtextutils | 0.7 | Gordon's Text utils Library | Mar 25, 2025 | AGPL |
| mafft | 7.313 | Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform | Mar 25, 2025 | BSD |
| mummer | 3.23 | MUMmer is a system for rapidly aligning entire genomes | Mar 25, 2025 | The Artistic License |
| pear | 0.9.11 | PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger | Mar 25, 2025 | CC-BY-NC-SA-3.0 |
| picard | 2.17.8 | Java tools for working with NGS data in the BAM format | Mar 25, 2025 | MIT |
| prinseq | 0.20.4 | PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data | Mar 25, 2025 | GPLv3 |
| pysam | 0.12.0.1 | Python module for reading and manipulating SAM/BAM/VCF/BCF files | Mar 25, 2025 | MIT |
| samtools | 1.3.1 | Tools for dealing with SAM, BAM and CRAM files | Mar 25, 2025 | MIT |
| smalt | 0.7.6 | SMALT aligns DNA sequencing reads with a reference genome. | Mar 25, 2025 | GPLv3 |
| sra-tools | 2.8.2.5 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | Mar 25, 2025 | Public Domain |
| swi-prolog | 7.7.5 | A comprehensive Prolog implementation | Mar 25, 2025 | BSD |
| tbb | 2018u2 | Intel(R) Threading Building Blocks (Intel TBB) | Mar 25, 2025 | Apache-2.0 |
| trimmomatic | 0.36 | A flexible read trimming tool for Illumina NGS data | Mar 25, 2025 | GPLv3 |