Rahul Nayak
A Bioinformatician
Our Sponsors
Related items
Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 2318 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large...
By Jit 1496 days agogithub.com - chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons. USAGE: -query: sequence A in fasta format -db: sequence B in fasta format -out: output matrix -kmer Integer: k>1...molinspiration: broad range of cheminformatics software tools supporting molecule manipulation
By BioJoker 2606 days agowww.molinspiration.com - Molinspiration offers broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation,...Jvarkit : Java utilities for Bioinformatics
By Jit 2832 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsCerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2835 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2804 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...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2730 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2675 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...
Evaluation of genome assembly software based on long reads
By BioStar 2594 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2216 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:
