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Utilities (next-generation sequencing)

Utilities for next-generation sequencing (NGS) analysis.

Utilities steps

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gdsfmt
Desktop

gdsfmt

Provides efficient, platform-independent memory and file management for…

Provides efficient, platform-independent memory and file management for genome-wide numerical data. gdsfmt provides genomic data structure (GDS) file format for array-oriented data. It is useful in…

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DNABarcodes
Desktop

DNABarcodes

Creates DNA barcode sets capable of correcting insertion, deletion, and…

Creates DNA barcode sets capable of correcting insertion, deletion, and substitution errors. DNABarcodes generates sets from a few basic input parameters (e.g. length, distance metric, minimum…

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CGAT
Desktop

CGAT Computational Genomics Analysis Toolkit

A collection of tools for the computational genomicist written in the python…

A collection of tools for the computational genomicist written in the python language. The tools have been developed and accumulated in various genome projects and NGS projects.

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Synergizer
Web

Synergizer

Provides translations of biological database identifiers. Synergizer offers a…

Provides translations of biological database identifiers. Synergizer offers a web app and an API accessible both programmatically and interactively. For each authority, it uses a peg that is specific…

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nanoraw
Desktop

nanoraw

Provides tools for the analysis of raw nanopore sequencing data, including…

Provides tools for the analysis of raw nanopore sequencing data, including correction of basecalls and visualization. Nanoraw primarily allows for the identification of modified DNA bases by…

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h5vc
Desktop

h5vc

A package that contains functions to interact with tally data from NGS…

A package that contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. h5vc contains functionality for creating tallies from BAM files, flexible and scalable…

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Genome…
Desktop

Genome Randomizer

Generates random sequences from complete prokaryotic genomes using 11 different…

Generates random sequences from complete prokaryotic genomes using 11 different stochastic models (rndb, rndm1, rndm3, rndm5, rndbb, rndbbp, rndm1m1, rndm1m1p, rmdm1c, rndm1c1, rndm3m3p). Genome…

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DICT
Web

DICT DAVID Gene ID Conversion Tool

Provides a comprehensive means for batch translations. DICT is a web based…

Provides a comprehensive means for batch translations. DICT is a web based application which covers dozens of commonly used types of gene and protein identifiers. It provides (i) enhanced translation…

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DiStats
Desktop

DiStats

Simplifies the task of preparing DNA barcode data releases. Among other…

Simplifies the task of preparing DNA barcode data releases. Among other statistics, DiStats computes intraspecific distances, data on closest species pairs, or on most distant congeners. It has an…

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Picopore
Desktop

Picopore

Reduces the storage footprint of the Oxford Nanopore Technologies (ONT) runs…

Reduces the storage footprint of the Oxford Nanopore Technologies (ONT) runs without preventing users from using their preferred analysis tools. Picopore is a software suite offering three methods of…

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HGVS
Desktop

HGVS

An open-source and easy-to-use Python library that facilitates the parsing,…

An open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the Human Genome Variation Society (HGVS) specification.…

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EMBOSS Seqret
Desktop
Web

EMBOSS Seqret

Reads and writes (returns) sequences. EMBOSS Seqret is useful for a variety of…

Reads and writes (returns) sequences. EMBOSS Seqret is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the…

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BioDOM
Desktop

BioDOM

Provides an easy way to build XML files following the Helmholtz Open…

Provides an easy way to build XML files following the Helmholtz Open BioInformatics Technology network (HOBIT) format descriptions from inside the user's own programs. BioDOM is designed to be a…

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BOLD
Web

BOLD Barcode of Life Data Systems

Aides the acquisition, storage, analysis and publication of DNA barcode…

Aides the acquisition, storage, analysis and publication of DNA barcode records. BOLD is a cloud-based data storage and analysis platform which consists of four main modules: a data portal, an…

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BiocFileCache
Desktop

BiocFileCache

Creates a persistent on-disk cache of files that the user can add, update, and…

Creates a persistent on-disk cache of files that the user can add, update, and retrieve. BiocFileCache is an R package useful for managing resources that are costly or difficult to create, web…

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KBWS
Web
Desktop

KBWS Keio Bioinformatics Web Service

Provides an EMBASSY (EMBOSS associated software) package for accessing popular…

Provides an EMBASSY (EMBOSS associated software) package for accessing popular bioinformatics web services. As an EMBOSS package, KBWS can be accessed from a number of graphical user interfaces…

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ID History…
Web

ID History Converter

Allows the user to input a list of Ensembl IDs from a previous Ensembl release,…

Allows the user to input a list of Ensembl IDs from a previous Ensembl release, and find what IDs they map to in the current release. ID History Converter allows the user to choose their species and…

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poreminion
Desktop

poreminion

Additional tools for analyzing Oxford Nanopore minION data. poreminion contains…

Additional tools for analyzing Oxford Nanopore minION data. poreminion contains some tools that have been made on top of Aaron R. Quinlan's and Nicholas J. Loman's poretools, and therefore…

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WebDSV
Web

WebDSV

Allows users to work on DNA sequences. WebDSV assists in creation, edition and…

Allows users to work on DNA sequences. WebDSV assists in creation, edition and analysis of DNA sequences. This tool enables visualization of sequences and permits user to mark them. It generates…

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XMLTool
Desktop

XMLTool

Offers a way for managing XML files. XMLTool is part of the QuiXoT Software…

Offers a way for managing XML files. XMLTool is part of the QuiXoT Software Package and aims to provide an efficient handling especially for large QuiXML files.

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Taxodb_ncbi
Desktop

Taxodb_ncbi

Allows to format the NCBI Taxonomy Database.

Allows to format the NCBI Taxonomy Database.

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Taxo_rrna
Desktop

Taxo_rrna

Allows to format Silva and Greengenes 16S databases.

Allows to format Silva and Greengenes 16S databases.

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NiBabel
Desktop

NiBabel

Furnishes a neuroimaging viewer. NiBabel provides an access to a wide range of…

Furnishes a neuroimaging viewer. NiBabel provides an access to a wide range of imaging formats. Besides, it contains functionality for writing annotation and morphometry files. The software allows…

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EDFlib
Desktop

EDFlib

Permits to view and edit EDF and BDF files.

Permits to view and edit EDF and BDF files.

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jugds
Desktop

jugds

Provides an interface to exploit CoreArray Genomic Data Structure (GDS) data…

Provides an interface to exploit CoreArray Genomic Data Structure (GDS) data files. jugds offers efficient operations to deal with single-nucleotide polymorphism (SNP).

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pygds
Desktop

pygds

Offers an interface to CoreArray Genomic Data Structure (GDS) data files. pygds…

Offers an interface to CoreArray Genomic Data Structure (GDS) data files. pygds permits to store multiple scalable array-oriented data sets enriched with metadata. It was especially created for…

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ID Converter…
Web

ID Converter System

Converts data IDs for biological molecules used in a database into other. The…

Converts data IDs for biological molecules used in a database into other. The ID Converter System is a system that does the batch conversion to ID of the form that specifies the input ID list.…

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dbigcg
Desktop

dbigcg

Indexes a GCG formatted database. dbigcg can build EMBL CD-ROM format index…

Indexes a GCG formatted database. dbigcg can build EMBL CD-ROM format index files. It will index the ID name and the accession number, if it’s present. If they are present in database, it can be…

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R-pbutils
Desktop

R-pbutils

An R package providing plotting and convenience functions.

An R package providing plotting and convenience functions.

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