Rahul Nayak
A Bioinformatician
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HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 574 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...
Run miniasm assembler on nanopore reads !
Last updated 3004 days ago by Jit Comments (5)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...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3024 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...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2855 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2881 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2827 days agowww.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 2173 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2713 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...Platanus
By Jit 3588 days ago Comments (1)platanus.bio.titech.ac.jp - Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 2382 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAP
