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htstream
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public |
HTStream is a quality control and processing pipeline for High Throughput Sequencing data.
The difference between HTStream and other tools is that HTStream uses a tab delimited fastq format that allows for streaming from application to application.
This streaming creates some awesome efficiencies when processing HTS data and makes it fully interoperable with other standard Linux tools.
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2025-01-16 |
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ndex2
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public |
Nice CX Python includes a client and a data model.
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2025-01-16 |
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rust-gtars
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public |
Performance-critical tools to manipulate, analyze, and process genomic interval data.
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2025-01-15 |
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mrtrix3
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public |
A set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
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2025-01-15 |
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arborator
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public |
Arborator: Simplifying operationalized pathogen surveillance and outbreak detection
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2025-01-15 |
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dnarrange
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public |
Find rearrangements in "long" DNA reads relative to a genome sequence
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2025-01-15 |
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gempipe
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public |
gempipe is a tool for the reconstruction of strain-specific genome-scale metabolic models.
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2025-01-15 |
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sourmash
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public |
Compute and compare MinHash signatures for DNA data sets.
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2025-01-15 |
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delly
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public |
Structural variant discovery by integrated paired-end and split-read analysis
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2025-01-15 |
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quantpi
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public |
A general profiling system focus on robust microbiome research
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2025-01-15 |
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homer
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public |
Software for motif discovery and next generation sequencing analysis
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2025-01-15 |
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lovis4u
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public |
Loci Visualisation Tool.
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2025-01-15 |
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snakebids
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public |
BIDS integration into snakemake workflows
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2025-01-15 |
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ncbi-vdb
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public |
SRA tools database engine.
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2025-01-15 |
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prymer
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public |
Python Primer Design Library
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2025-01-14 |
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eva-sub-cli
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public |
EVA Submission Command Line Interface
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2025-01-14 |
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varlociraptor
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public |
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
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2025-01-14 |
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muscle
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public |
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences
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2025-01-14 |
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pasta
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public |
An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm
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2025-01-14 |
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biobb_godmd
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public |
Biobb_godmd is a BioBB category for GOdMD tool (protein conformational transitions).
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2025-01-14 |
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biobb_flexserv
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public |
Biobb_flexserv is the Biobb module collection for biomolecular flexibility studies on protein 3D structures.
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2025-01-14 |
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seg-suite
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public |
The seg suite provides tools for manipulating segments, alignments, and annotations of sequences.
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2025-01-14 |
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perl-bio-phylo
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public |
An object-oriented Perl toolkit for analyzing and manipulating phyloinformatic data.
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2025-01-14 |
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agat
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public |
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
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2025-01-14 |
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ensembl-vep
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public |
Ensembl Variant Effect Predictor
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2025-01-14 |
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abricate
|
public |
Mass screening of contigs for antibiotic resistance genes
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2025-01-14 |
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mirdeep2
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public |
A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs
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2025-01-14 |
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unitas
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public |
unitas is a convenient tool for efficient annotation of small non-coding RNA sequence datasets produced by Next Generation Sequencing.
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2025-01-14 |
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srax
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public |
Systematic Resistome Analysis
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2025-01-14 |
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dialign-tx
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public |
DIALIGN-TX is a greedy and progressive approaches for segment-based multiple sequence alignment
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2025-01-14 |
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ngmlr
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public |
ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore reads to a reference genome and optimized for structural variation detection
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2025-01-14 |
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poppunk
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public |
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
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2025-01-13 |
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ngscheckmate
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public |
Software package for identifying next generation sequencing (NGS) data files from the same individual.
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2025-01-13 |
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gffread
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public |
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.
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2025-01-13 |
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quantms-rescoring
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public |
PSM rescoring python package with scripts and helpers for the quantms workflow
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2025-01-13 |
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viloca
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public |
VILOCA is a tool to analyse short- and long-read sequencing viral samples. It provides mutation calls and local haplotypes.
|
2025-01-13 |
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flams
|
public |
Find Lysine Acylation & other Modification Sites
|
2025-01-13 |
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teloscope
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public |
A telomere annotation tools for genome assemblies
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2025-01-13 |
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scib
|
public |
Evaluating single-cell data integration methods
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2025-01-13 |
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svision-pro
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public |
Neural-network-based long-read SV caller.
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2025-01-13 |
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pydeseq2
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public |
A python implementation of DESeq2.
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2025-01-13 |
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isoquant
|
public |
IsoQuant is a tool for reference-based analysis of long RNA reads, such as gene/transcript quantification and discovery.
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2025-01-13 |
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gottcha2
|
public |
Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2
|
2025-01-13 |
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msoma
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public |
mSOMA: Somatic Mutation Detection using a betabinomial null model
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2025-01-13 |
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fast2q
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public |
A Python3 program that counts sequence occurrences in FASTQ files.
|
2025-01-13 |
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unicore
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public |
Universal and efficient core gene phylogeny with Foldseek and ProstT5
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2025-01-13 |
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pyfastani
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public |
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
|
2025-01-13 |
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argo
|
public |
Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping
|
2025-01-13 |
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perl-graph
|
public |
a Perl extension for keeping data partially sorted
|
2025-01-13 |
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dnaapler
|
public |
Reorients assembled microbial sequences
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2025-01-13 |
