Rahul Nayak
A Bioinformatician
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LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2952 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3492 days agoStructural variation caller tools using long readsminiasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3235 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...
Evaluation of genome assembly software based on long reads
By BioStar 2804 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...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 2466 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 3508 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 3233 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2940 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...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 2032 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 3052 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...
