Rahul Nayak
A Bioinformatician
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Graph Genome Suite
By Jit 2948 days agowww.sbgenomics.com - Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development and precision medicine. We build self-improving systems to analyze millions of genomes, including the Graph...R Graphical Cookbook by Winston Chang
By Abhimanyu Singh 2941 days agoR Graphical Cookbook by Winston Chang A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown...SWALO
By Jit 2915 days agoatifrahman.github.io - SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Download Git repository of SWALO is at...Cutadapt
By Bulbul 2901 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an...HTSlib
By Jit 2810 days agohttp://www.htslib.org/ - Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing BCF2/VCF/gVCF files and...Fastq format
By Jit 2762 days agoen.wikipedia.org - FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a...
Quick next generation sequencing (NGS) terms definition
Last updated 2725 days ago by Neelfragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants,...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2550 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,...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2370 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...RNA-seq Analysis Workshop Course Materials
By Jit 2335 days agochagall.med.cornell.edu - RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves...
