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SplicePlot is a tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files.
Galaxy's data integration platform supports file uploads from the user's computer, by URL, and directly from many online external resources (such as the UCSC Genome Browser, BioMart and InterMine). Galaxy supports a range of widely used biological data formats, translation between those formats, and data conversions (see Tools).
The Biopython project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers. [ 1 ] [ 4 ] [ 5 ] It contains classes to represent biological sequences and sequence annotations , and it is able to read and write to a variety of file formats.
Linux, macOS, Windows: BSD: Laura Luebbert and Lior Pachter: GROMACS: Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. Linux, macOS, Windows: Common Public 1.0 GenoViz Integrated Genome Browser: Java-based desktop genome browser: Linux, macOS, Windows: Common Public 1.0 GenoViz InterMine
The index command creates a new index file that allows fast look-up of data in a (sorted) SAM or BAM. Like an index on a database, the generated *.sam.sai or *.bam.bai file allows programs that can read it to more efficiently work with the data in the associated files. tview
Accurately performs gapped alignment of sequence data obtained from next-generation sequencing machines (specifically of Solexa-Illumina) back to a genome of any size. Includes adaptor trimming, SNP calling and Bisulfite sequence analysis. Yes, also supports Illumina *_int.txt and *_prb.txt files with all 4 quality scores for each base
A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing: Yes: Yes: sourcecode [186] Colorstock, SScolor, Raton: Colorstock, a command-line script using ANSI terminal color; SScolor, a Perl script that generates static HTML pages; and Raton, an Ajax web application generating dynamic HTML. Each tool can be used to color ...
SPAdes keeps a data structure to be able to backtrack all corrections or removals. SPAdes modifies the previously used bulge removal approach [ 16 ] and iterative de Bruijn graph approach from Peng et al (2010) [ 17 ] and creates a new approach called ‘‘bulge corremoval’’, which stands for bulge correction and removal.