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GTF/GFF file manipulation bioinformatics software tools

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Cufflinks
Desktop

Cufflinks

Assembles transcripts, estimates their abundances, and tests for differential…

Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

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BEDTools
Desktop

BEDTools

A software suite for the comparison, manipulation and annotation of genomic…

A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of…

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NGSUtils
Desktop

NGSUtils

A suite of software tools for manipulating data common to next-generation…

A suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. With modules that operate from FASTQ pre-processing through…

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GFF3sort
Desktop

GFF3sort

Produces sorting results that could be correctly rendered by JBrowse while…

Produces sorting results that could be correctly rendered by JBrowse while saving a significant amount of time. GFF3sort is an efficient script written in Perl to sort GFF3 files for tabix indexing.…

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GFFview
Web

GFFview

Allows to parse the annotation information of eukaryotic genome and then…

Allows to parse the annotation information of eukaryotic genome and then generate statistical description of six indices for visualization. GFFview Was developed in order to investigate quality and…

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GFF3toEMBL
Desktop

GFF3toEMBL

Converts files from the prokaryote annotation tool Prokka to a format which can…

Converts files from the prokaryote annotation tool Prokka to a format which can be submitted to EMBL. GFF3toEMBL cannot be applied as a generic conversion tool and only implements some EMBL…

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gff2sequence
Desktop

gff2sequence

Provides a valuable alternative for the generation of a customized sequence…

Provides a valuable alternative for the generation of a customized sequence dataset from general feature formatted file. gff2sequence is an open-source program which allows the extraction of gene…

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PileLine
Desktop

PileLine

Implements a flexible command-line toolkit providing specific support to the…

Implements a flexible command-line toolkit providing specific support to the management, filtering, comparison and annotation of genomic position (GP) files produced by next generation sequencing…

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RACKJ
Desktop

RACKJ Read Analysis & Comparison Kit in Java

A set of Java programs that analyze and compare RNA-seq data made by NGS…

A set of Java programs that analyze and compare RNA-seq data made by NGS technologies. In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing…

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gffutils
Desktop

gffutils

Manipulates Gene Finding Format (GFF) and Gene Transfer Format (GTF) files to…

Manipulates Gene Finding Format (GFF) and Gene Transfer Format (GTF) files to extract data. gffutils can build a database to infer the gene and transcript extents. It offers features to convert…

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LibGFF
Desktop

LibGFF

Provides a simple General Feature Format (GFF) and General Transfer Format…

Provides a simple General Feature Format (GFF) and General Transfer Format (GTF) parsing resource. LibGFF is a library that provides GTF/GFF parsers exposing a C++ interface without the necessity of…

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Cuffquant
Desktop

Cuffquant

Permits users to estimate isoform expression. Cuffquant is able to ignore…

Permits users to estimate isoform expression. Cuffquant is able to ignore alignments not structurally compatible with any reference transcript. It requires users to attach custom tags to individual…

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Cuffmerge
Desktop

Cuffmerge

Merges several Cufflinks assemblies. Cuffmerge can automatically filter a…

Merges several Cufflinks assemblies. Cuffmerge can automatically filter a number of transfrags that are probably artefacts. It makes it easier to make an assembly GTF file suitable for use with…

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Cuffcompare
Desktop

Cuffcompare

Provides a way to analyze assembled transfrags. Cuffcompare permits users to…

Provides a way to analyze assembled transfrags. Cuffcompare permits users to face assembled transcripts with a reference annotation. It returns various statistics related to the “accuracy” of the…

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File Chameleon
Web

File Chameleon

Assists in reformatting existing genomic flat files. File Chameleon…

Assists in reformatting existing genomic flat files. File Chameleon doesn't convert formats or merge files, only modifies existing files already available on the Ensembl FTP site. It tries to…

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