Curator Dashboard

Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for finding, investigating, loading and disseminating data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library to generate images for odontograms.Allows to choose between png or jpg images.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s).

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth