Rahul Nayak
A Bioinformatician
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Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2821 days agoStructural variation caller tools using long readsPorechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2381 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...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2298 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2298 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....Platanus
By Jit 3127 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...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2534 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...Ranbow: a haplotype assembler for polyploid genomes
By Jit 2378 days agowww.molgen.mpg.de - Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing,...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1978 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...Shasta long read assembler
By Jit 1786 days ago Comments (1)github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2298 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....
