Jit
Enthusiast computational biologist with business dream !!!
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SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
By Jit 2998 days agogithub.com - SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically...S-plot2: creates an interactive, two-dimensional heatmap of sequences
By Jit 2717 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2642 days agolbbe.univ-lyon1.fr - The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome...
By Jit 2454 days agogithub.com - Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding...Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism
By Rahul Nayak 2204 days agoMCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal...IgBLAST 1.17 is now available with improved identification of productive V gene sequences
By Jit 1952 days agoIgBLAST 1.17 is now available with improved identification of productive V gene sequencesSteps to find palindrome in genomes !
By BioStar 1094 days agoPalindromes are sequences of nucleotides that read the same backward as forward.Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By Neel 205 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies. The performance of the Jaeger...EAGLER: a scaffolding tool for long reads.
By Jit 2833 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2801 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...
