Rahul Nayak
A Bioinformatician
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BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 2826 days agowww.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...MITOS: improved de novo metazoan mitochondrial genome annotation
By Jit 2689 days agomitos.bioinf.uni-leipzig.de - Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene...Look up a biological numbers
By Jitendra Narayan 4579 days agobionumbers.hms.harvard.edu - Did you ever need to look up a number like the volume of a cell or the cellular concentration of ATP, only to find yourself spending much more time than you wanted on the Internet or flipping through textbooks - all without much...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2825 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,...1mb long DNA with Nanopore technology
By Jit 2999 days agoLongest read of 1mb achievements with Nanopore
Read Simulators
Last updated 1254 days ago by Abhi Comments (1)Short Read Simulators With the popularity of next-generation sequencing (NGS) technologies, many NGS read simulators have been developed. Currently, many of the popular short read simulators are designed to simulate reads mimicking many Illumina,...proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
By Jit 2983 days agogithub.com - proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2822 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2754 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...URMAP, an ultra-fast read mapper
By Jit 1954 days ago Comments (1)github.com - URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves...
