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rust-bio-tools
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public |
A growing collection of fast and secure command line utilities for dealing with NGS data
implemented on top of Rust-Bio.
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2025-09-18 |
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abyss
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public |
Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.
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2025-09-18 |
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pantools
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public |
PanTools is a pangenomic toolkit for comparative analysis of large numbers of genomes.
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2025-09-18 |
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beagle
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public |
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
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2025-09-18 |
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filtlong
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public |
Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
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2025-09-18 |
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trinity
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public |
Trinity assembles transcript sequences from Illumina RNA-Seq data.
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2025-09-18 |
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snap-aligner
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public |
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
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2025-09-17 |
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dsrc
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public |
high-performance compression of sequencing reads stored in FASTQ format
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2025-09-16 |
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bamutil
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public |
Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
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2025-09-16 |
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nonpareil
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public |
Estimate average coverage and create curves for metagenomic datasets
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2025-09-16 |
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idba
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public |
IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
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2025-09-16 |
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advntr
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public |
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
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2025-09-16 |
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zerone
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public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
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2025-09-16 |
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yass
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public |
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format.
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2025-09-16 |
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genepop
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public |
Population Genetic Data Analysis package.
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2025-09-16 |
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snp-sites
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public |
Finds SNP sites from a multi-FASTA alignment file.
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2025-09-16 |
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clever-toolkit
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public |
The clever toolkit (CTK) is a suite of tools to analyze next-generation sequencing data and, in particular, to discover and genotype insertions and deletions from paired-end reads.
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2025-09-16 |
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r-spp
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public |
Analysis of ChIP-seq and other functional sequencing data [Kharchenko PV (2008) <DOI:10.1038/nbt.1508>].
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2025-09-16 |
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fraggenescan
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public |
FragGeneScan is an application for finding (fragmented) genes in short reads.
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2025-09-16 |
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elprep
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public |
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
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2025-09-16 |
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bamm
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public |
Metagenomics-focused BAM file manipulation
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2025-09-16 |
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perl-math-base-convert
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public |
Very fast base to base conversion.
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2025-09-16 |
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gmap
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public |
Genomic mapping and alignment program for mRNA and EST sequences.
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2025-09-15 |
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sonicparanoid
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public |
SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models
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2025-09-15 |
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perl-mime-types
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public |
Definition of MIME types
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2025-09-15 |
