Comment on "Short-read assembly using Spades !"
Short-read assembly is the process of constructing a genome sequence from a large number of short sequencing reads. SPAdes (St. Petersburg genome assemb...431 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
Genome synteny analysis is the comparison of the genomic structure and gene content of two or more related species. Here are some general steps to follow for conducting a g...438 days ago
Comment on "Basic command-line to run BLAST"
Following steps need to followed while doing any homology search. BLAST (Basic Local Alignment Search Tool) is a widely used program for searchin...438 days ago
Comment on "List of non-commercial NGS genotype-calling software"
Delly – Structural variant discovery by integrated paired-end and split-read analysis. [ paper-2012 ] lumpy – lumpy: a general probabilisti...1158 days ago
Comment on "SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator"
Another nice simulation tool https://bioinformaticsonline.com/bookmarks/view/40302/simug-a-general-purpose-genome-simulator1416 days ago
Comment on "Genome in a Bottle (GIAB) Consortium"
Benchmark (or "High-confidence") variant calls and regions:We developed an integration pipeline to utilize sequencing data generated by multiple technologies to generate va...1575 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
.... [false] -B, --batch-mb INT Reads will be loaded in batches of the size specified in megabytes. Value <= 0 loads the entire file. [1024] General-purpose pre-set options: -x, --preset...2307 days ago
Comment on "Structural variation: the hidden genomic treasure"
Hydra-SV The pipeline described below is meant to convey a general approach that they have found to be effective for discovering SV breakpoints with Hydra. However, it...2718 days ago
Comment on "Commercial and public next-gen-seq (NGS) software"
There are several other softwares Eland: http://illumina.ucr.edu/illumina_docs/Velvet:http://www.ebi.ac.uk/~zerbino/velvet/Maq (Mapping and Assembly with Quality): http://...3637 days ago
Comment on "R and Bioconductor Tutorial"
SimpleR tutorials is very lucid and practical for general data analysis with R. http://cran.r-project.org/doc/contrib/Verzani-SimpleR.pdf3722 days ago