Search Results for "format tool"
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Showing 37 open source projects for "format tool"
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Bowtie 2
A fast and sensitive gapped read aligner
...It is especially effective for reads ranging from around 50 bases to hundreds or thousands of characters, and it supports modern sequencing workflows that require gapped, local, and paired-end alignment. The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. ... -
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CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
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ParDRe
Parallel tool to remove duplicate DNA reads
ParDRe is a parallel tool to remove duplicate reads. Duplicate reads can be seen as identical or nearly identical sequences with some mismatches. This tool will let the users to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset (e.g., assemblies, mappings, etc.). The tool is implemented with MPI in order to exploit the parallel capabilities of multicore clusters. -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
...MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. ... -
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
...TaxOnTree also corrects for the absence of some taxa in NCBI taxonomy. Command line program is easy to set up and can be coupled to several bioinformatics tools, producing a colored tree in PDF format. TaxOnTree is available as a web tool in http://biodados.icb.ufmg.br/taxontree for low demanding jobs. -
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DrawGlycan-SNFG
Renders glycans and glycopeptides with frag. info using SNFG format
DrawGlycan-SNFG is a simple and robust drawing tool for displaying glycans and glycopeptides from IUPAC-condensed format text inputs. It also supports the depiction of glycan and glycopeptide fragmentation. The program is available in the form of web (link below) and standalone GUI applications. Program source code is also provided.. The web and GUI apps do not require any additional software to run. -
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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
...Formats which can be generated by fcGENE: plink-pedigree, plink-raw, plink-dosage, mach-inputs, minimac-inputs, impute-inputs, beagle-inputs and bimbam-inputs, HAPLOVIEW-inputs, EIGENSOFT-inputs. Further application: -obtaining templates of necessary imputation commands and commands of other imputation tool - Quality control according as MAF,HWE & CALLRATE. key words: genotype transformation, convert genotype format, imputation output, PLINK, IMPUTE, MACH, minimac, HAPLOVIEW, BEAGLE, BIMBAM,EIGENSOFT. -
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...The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http://samtools.github.io/hts-specs/VCFv4.2.pdf). HTDP provides quick filtering functionality and can process data consisting of single or multiple input files. Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. ...
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PBSuite
Software for Long-Read Sequencing Data from PacBio
This currently hosts two projects created and maintained by Adam English. PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads. ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. ... -
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data.... -
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result).... -
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(NCS) NEQUIM Contact System
Tool for analyze of interactions in ligand-protein complexes
NEQUIM Contact System (NCS) is a system to generate and analyze interaction vectors of protein-ligand complexes. Core features include multiple views of vectors, multiple selection options, cluster analysis and generation of interaction vector model. The input could be from PDB format or from files generated by automatic docking softwares AutoDock/Vina or Surflex. -
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Sequencia
Protein Primary Sequnece Analysis
...This work includes all the Physiochemical Properties- related to Primary Sequence Analysis under a common platform. JAVA, BIOJAVA were used under Platform Independent architecture. The Tool includes Properties of being offline where result can be stored in Text Format, here we can paste more than one sequence and also upload FASTA file to compute Parameters. -
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...It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv and txt format. The software source code is freely available under the license of GPL2.
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SAMSVM
A tool for misalignment filtration on SAM-format sequences with SVM
Applying the LIBSVM, a package of support vector machine, SAMSVM was developed to correctly detect and filter the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis. -
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand proteins' : 1. ... -
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. ...
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BIRAP
Bacterial Intergenic Region Analysis Pipeline
...When information regarding the locus of promot-ers and terminators in the genome (in .coords format) is pro-vided, the pipeline will also help identify non-coding RNA. -
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade-defining polymorphism. ... -
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SyntheticWSI
Tools to generate and visualize artificial whole slide images
Java 8+ required. Collection of tools to help generate artificial Whole Slide Images (WSIs). A WSI is stored as a ZIP archive of JPG tiles, and this software contains a tool to visualize this format. SVS files can be used directly for texture extraction (thanks to the included Bio-Formats library). Main source files in package fr.unistra.wsi.synthetic. -
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TUIT
Taxonomic Unit Identification Tool
For the installation instructions please see Wiki page: https://sourceforge.net/p/tuit/wiki/ IMPORTANT: since version 1.0.4.0 TUIT allows to select RDP-like formatted output to improve out of the box compatability with tools, that assume RDP-formatted input. A new field has been added to the properties.xml, please make sure to update it to contain <OutputFormat format="tuit"/> or <OutputFormat format="rdp"/> in the <BLASTNParameters> section. Read our paper in Biotechniques: http://www.ncbi.nlm.nih.gov/pubmed/24502797 Taxonomic Unit Identification Tool (TUIT) is a free open source platform-independent software, designed specifically to facilitate taxonomic annotation of nucleotide sequences via BLAST homology search against the NCBI databases. ... -
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Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
