Jit
Enthusiast computational biologist with business dream !!!
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PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2560 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 1609 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...Ancestral sequence reconstruction (ASR) or ancestral gene/sequence reconstruction/resurrection...
By Jit 2745 days ago Comments (2)Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolutionlordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2199 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...LAMSA: fast split read alignment with long approximate matches
By Jit 2395 days ago Comments (1)github.com - LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes takes the...Mulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 2694 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...CLARK: Fast, accurate and versatile sequence classification system
By Jit 1755 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...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 2343 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...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 2752 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...
