Rahul Nayak
A Bioinformatician
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CABOG: Celera Assembler with Best Overlap Graph
By Abhimanyu Singh 3308 days agowww.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...Installing Bandage on Ubunty !
By Jit 2950 days agoinstructions successfully build Bandage on a fresh installation of Ubuntu 14.04Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2526 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...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3369 days agoStructural variation caller tools using long readsHISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 2950 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...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3112 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 2681 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 2343 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...Harvest
By Jit 3412 days agoharvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...splitbam: splits a BAM by chromosomes
By Jit 3384 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...
