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The Role of lncRNA in Bioinformatics: Unlocking the Secrets of the Genome
By LEGE 456 days agolncRNAs are the hidden gems of the genome, and bioinformatics is the key to unearthing their full potential. As research progresses, lncRNAs could pave the way for novel diagnostics, targeted therapies, and personalized medicine, revolutionizing...NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design
By BioStar 379 days agoNVIDIA and the Arc Institute have introduced Evo 2, a groundbreaking AI model designed to understand, predict, and generate DNA sequences. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode...LAMSA: fast split read alignment with long approximate matches
By Jit 2853 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...nanofilt: Filtering and trimming of long read sequencing data
By Jit 2777 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...COSINE: non-seeding method for mapping long noisy sequences
By Jit 2690 days agogithub.com - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq...
By LEGE 1633 days agogithub.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2657 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...Reference-free prediction of rearrangement breakpoint reads
By Neel 2921 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2845 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from...
By Jit 2825 days agogithub.com - Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by...
