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https://hub.docker.com/r/biodepot/star-for-criu/
Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.
Proper citation: star-for-criu (RRID:SCR_016294) Copy
http://sourceforge.net/projects/bbmap
Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.
Proper citation: BBmap (RRID:SCR_016965) Copy
Software designed to automatically realign brain images for easier cross patient examination regardless of age, disease or head position. It positions and aligns anatomy-related sagittal, coronal and axial slices using anatomical landmarks.
Proper citation: AutoAlign Head (RRID:SCR_014245) Copy
https://github.com/ruanjue/wtdbg2.git
Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.
Proper citation: WTDBG (RRID:SCR_017225) Copy
http://wasabiapp.org/software/prank/
Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.
Proper citation: prank (RRID:SCR_017228) Copy
http://clustalw.ddbj.nig.ac.jp/index.php
Web sevice of ClustalW provided by DNA data bank of Japan.
Proper citation: ClustalW (RRID:SCR_017277) Copy
http://www.ebi.ac.uk/Tools/msa/muscle/
Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.
Proper citation: MUSCLE (RRID:SCR_011812) Copy
https://github.com/schloi/MARVEL
Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads.
Proper citation: Marvel (RRID:SCR_017621) Copy
http://www.imgt.org/HighV-QUEST/home.action
Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.
Proper citation: IMGT HighV-QUEST (RRID:SCR_018196) Copy
https://github.com/marbl/MashMap
Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.
Proper citation: MashMap (RRID:SCR_022194) Copy
http://dissect-trans.sourceforge.net/Home
Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.
Proper citation: Dissect (RRID:SCR_000058) Copy
https://github.com/jeffdaily/parasail
Software tool as multiple sequence alignement for global, local and semi global alignments.
Proper citation: PARASAIL (RRID:SCR_021805) Copy
https://github.com/Gaius-Augustus/learnMSA
Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded.
Proper citation: learnMSA (RRID:SCR_022572) Copy
Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.
Proper citation: ProDA (RRID:SCR_024171) Copy
https://github.com/biocore/pynast
Software tool for aligning sequences to template alignment.
Proper citation: pynast (RRID:SCR_024189) Copy
https://www.imsc.res.in/~rsidd/sigma/
Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.
Proper citation: sigma-align (RRID:SCR_024337) Copy
https://github.com/ArtRand/signalAlign
Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments,
Proper citation: signalalign (RRID:SCR_024339) Copy
https://github.com/Martinsos/edlib
Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.
Proper citation: Edlib (RRID:SCR_024078) Copy
https://github.com/philres/ngmlr
Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection.
Proper citation: Ngmlr (RRID:SCR_017620) Copy
https://noblis.org/bioportal/tools.html
Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes.
Proper citation: BioVelocity (RRID:SCR_018501) Copy
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