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nematodes.org - Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for...

bioinfo.noble.org - GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data...

github.com - Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes...

darkhorse.ucsd.edu - DarkHorse is a bioinformatic method for rapid, automated identification and ranking of phylogenetically atypical proteins on a genome-wide basis. It works by selecting potential ortholog matches from a reference database of amino acid...

github.com - Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main...

Linux Commands Cheat Sheet    File System    ls — list items in current directory    ls -l — list items in current directory and show in long format to see perimissions, size, an modification...

broadinstitute.github.io - Decoding SAM flags This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties. To decode a given SAM flag...

kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...

github.com - CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R and python in background for specific modules....

These are just a scant few of the common questions asked by bioinformatics students as they ready themselves for the next exam sitting