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sequencetools
|
public |
A tool (pileupCaller) for processing ancient DNA sequencing data
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2025-01-30 |
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perl-libwww-perl
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public |
The World-Wide Web library for Perl.
|
2025-01-29 |
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perl-lwp-simple
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public |
simple procedural interface to LWP
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2025-01-29 |
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bioconda-utils
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public |
Utilities for building and managing bioconda recipes.
|
2025-01-29 |
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maxbin2
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public |
MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
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2025-01-29 |
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flashlfq
|
public |
Ultrafast label-free quantification algorithm for mass-spectrometry proteomics.
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2025-01-29 |
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perl-html-parser
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public |
HTML parser class
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2025-01-29 |
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bioconductor-biocgenerics
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public |
S4 generic functions used in Bioconductor
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2025-01-29 |
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bioconductor-copynumber
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public |
Segmentation of single- and multi-track copy number data by penalized least squares regression.
|
2025-01-29 |
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bioconductor-genomeinfodb
|
public |
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
|
2025-01-29 |
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bioconductor-iranges
|
public |
Foundation of integer range manipulation in Bioconductor
|
2025-01-29 |
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bioconductor-xvector
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public |
Foundation of external vector representation and manipulation in Bioconductor
|
2025-01-29 |
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bioconductor-s4vectors
|
public |
Foundation of vector-like and list-like containers in Bioconductor
|
2025-01-29 |
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bioconductor-zlibbioc
|
public |
An R packaged zlib-1.2.5
|
2025-01-29 |
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pairix
|
public |
2D indexing on bgzipped text files of paired genomic coordinates
|
2025-01-28 |
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egglib
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public |
Evolutionary Genetics and Genomics Library. EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, and coalescent simulations. EggLib is a flexible Python module with a performant underlying C++ library and allows fast and intuitive development of Python programs and scripts.
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2025-01-28 |
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pybigwig
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public |
A python extension written in C for quick access to bigWig files.
|
2025-01-28 |
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nf-core
|
public |
Python package with helper tools for the nf-core community.
|
2025-01-27 |
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poppunk
|
public |
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
|
2025-01-27 |
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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 |
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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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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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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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
abricate
|
public |
Mass screening of contigs for antibiotic resistance genes
|
2025-01-14 |
