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unicycler
|
public |
Hybrid assembly pipeline for bacterial genomes
|
2025-01-27 |
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miniasm
|
public |
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
|
2025-01-27 |
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perl-io-interactive
|
public |
Utilities for interactive I/O
|
2025-01-27 |
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py2bit
|
public |
A package for accessing 2bit files using lib2bit
|
2025-01-26 |
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solvebio
|
public |
The SolveBio Python client
|
2025-01-24 |
|
gdc-client
|
public |
GDC Data Transfer Tool
|
2025-01-24 |
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cat
|
public |
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
|
2025-01-24 |
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kma
|
public |
KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
|
2025-01-24 |
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rnastructure
|
public |
RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.
|
2025-01-23 |
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parsnp
|
public |
Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.
|
2025-01-23 |
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perl-math-bigint
|
public |
Arbitrary size floating point math package
|
2025-01-23 |
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openms
|
public |
OpenMS is an open-source software C++ library for LC-MS data management and analyses
|
2025-01-23 |
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spaln
|
public |
Map and align a set of cDNA/EST or protein sequences onto a genome
|
2025-01-23 |
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khmer
|
public |
khmer k-mer counting library
|
2025-01-23 |
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itsxpress
|
public |
ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files.
|
2025-01-22 |
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ectyper
|
public |
ECtyper is a python program for serotyping E. coli genomes
|
2025-01-22 |
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deeptoolsintervals
|
public |
A python module creating/accessing GTF-based interval trees with associated meta-data
|
2025-01-22 |
|
perl-socket
|
public |
networking constants and support functions
|
2025-01-22 |
|
whatshap
|
public |
Phase genomic variants using DNA sequencing reads (haplotype assembly).
|
2025-01-22 |
|
iced
|
public |
The python module iced implements the ICE normalization of hic data.
|
2025-01-22 |
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kleborate
|
public |
Kleborate: a tool for typing and screening pathogen genome assemblies
|
2025-01-21 |
|
sra-tools
|
public |
The SRA Toolkit and SDK from NCBI.
|
2025-01-21 |
|
igv
|
public |
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics
data and annotations.
|
2025-01-21 |
|
nextflow
|
public |
A DSL for data-driven computational pipelines http://nextflow.io
|
2025-01-21 |
|
deeptools
|
public |
A set of user-friendly tools for normalization and visualzation of deep-sequencing data
|
2025-01-20 |
|
mmseqs2
|
public |
MMseqs2: ultra fast and sensitive sequence search and clustering suite
|
2025-01-18 |
|
libbigwig
|
public |
A C library for handling bigWig files
|
2025-01-17 |
|
bioconductor-biostrings
|
public |
Efficient manipulation of biological strings
|
2025-01-17 |
|
last
|
public |
LAST finds & aligns related regions of sequences.
|
2025-01-16 |
|
bbmap
|
public |
BBMap is a short read aligner, as well as various other bioinformatic tools.
|
2025-01-16 |
|
htstream
|
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.
|
2025-01-16 |
|
sourmash
|
public |
Compute and compare MinHash signatures for DNA data sets.
|
2025-01-15 |
|
delly
|
public |
Structural variant discovery by integrated paired-end and split-read analysis
|
2025-01-15 |
|
homer
|
public |
Software for motif discovery and next generation sequencing analysis
|
2025-01-15 |
|
ncbi-vdb
|
public |
SRA tools database engine.
|
2025-01-15 |
|
muscle
|
public |
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences
|
2025-01-14 |
|
pasta
|
public |
An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm
|
2025-01-14 |
|
perl-bio-phylo
|
public |
An object-oriented Perl toolkit for analyzing and manipulating phyloinformatic data.
|
2025-01-14 |
|
ensembl-vep
|
public |
Ensembl Variant Effect Predictor
|
2025-01-14 |
|
abricate
|
public |
Mass screening of contigs for antibiotic resistance genes
|
2025-01-14 |
|
mirdeep2
|
public |
A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs
|
2025-01-14 |
|
unitas
|
public |
unitas is a convenient tool for efficient annotation of small non-coding RNA sequence datasets produced by Next Generation Sequencing.
|
2025-01-14 |
|
ngmlr
|
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
|
2025-01-14 |
|
gffread
|
public |
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.
|
2025-01-13 |
|
perl-graph
|
public |
a Perl extension for keeping data partially sorted
|
2025-01-13 |
|
perl-experimental
|
public |
Experimental features made easy
|
2025-01-09 |
|
bioconductor-pcaexplorer
|
public |
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
|
2025-01-08 |
|
perl-config-general
|
public |
Generic Config Module
|
2025-01-08 |
|
selene-sdk
|
public |
Framework for developing sequence-level deep learning networks.
|
2025-01-07 |
|
stacks
|
public |
Stacks is a software pipeline for building loci from short-read sequences.
|
2025-01-07 |
