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https://github.com/brentp/duphold
Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data.
Proper citation: duphold (RRID:SCR_016938) Copy
http://www.uimcimes.es/contenidos/golink?p=1
Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.
Proper citation: QModeling (RRID:SCR_016358) Copy
https://chlorobox.mpimp-golm.mpg.de/OGDraw.html
Software package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers.
Proper citation: OGDraw (RRID:SCR_017337) Copy
http://bioinformatics.uni-muenster.de/tools/nanopipe2
Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.
Proper citation: NanoPipe (RRID:SCR_016852) Copy
http://deweylab.biostat.wisc.edu/detonate/
Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.
Proper citation: DETONATE (RRID:SCR_017035) Copy
http://www.ebi.ac.uk/Tools/blast2/index.html
It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes.
Proper citation: Washington University Basic Local Alignment Search Tool (RRID:SCR_008285) Copy
Ratings or validation data are available for this resource
Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
Proper citation: GENCODE (RRID:SCR_014966) Copy
https://github.com/asdcid/Gene-conservation-informed-contig-alignment
Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity.
Proper citation: Gene-conservation-informed-contig-alignment (RRID:SCR_017617) Copy
https://github.com/cobilab/altair
Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events.
Proper citation: AltaiR (RRID:SCR_024752) Copy
https://github.com/liukai5016/FungiLT
Software classifier tool based on deep learning methods for classification and annotation of large-scale fungal ITS sequences. Used for fungal species classification.
Proper citation: FungiLT (RRID:SCR_025886) Copy
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