Rahul Nayak
A Bioinformatician
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Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2434 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...CNIDARIA: fast, reference-free phylogenomic clustering
By Shruti Paniwala 3762 days agogithub.com - Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2648 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 3230 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 3072 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
By Jit 3005 days ago Comments (1)github.com - FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise...Kalign: fast multiple sequence alignment program for biological sequences.
By BioStar 2530 days agogithub.com - Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 2109 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 940 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...New born babies get ready to know their whole genome soon!!!
By Rahul Agarwal 4778 days agoSequencing of hundreds of newborns
