BioStar
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AlfaPang: alignment free algorithm for pangenome graph construction
By BioStar 383 days agogithub.com - AlfaPang constructs variation graphs, leveraging its alignment-free and reference-free approach, based solely on intrinsic sequence properties. This design allows AlfaPang's runtime and memory usage to scale linearly with the size of input...FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 3202 days agowww.isical.ac.in - Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a...AnchorWave
By Neel 1665 days agogithub.com - AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor...RNA Bioinformatics and High Throughput Analysis Jena
Research Topics: High Throughput Sequencing Analysis Comparative Genomics Identification and Annotation of Non-coding RNAs Bioinformatic Analysis and System Biology of Viruses Coevolution of Proteins and RNAs Algorithmic...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2993 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...FLAS: fast and high throughput algorithm for PacBio long read self-correction.
By Jit 2642 days agogithub.com - FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes...MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3769 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
By BioStar 2374 days agogithub.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3794 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...mafTools
By Radha Agarkar 3768 days agogithub.com - Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
