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...
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...
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....
decipher.cee.wisc.edu - DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequence data. To install DECIPHER, see the Downloads page. To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the...
https://arvados.org/ - Arvados is a free and open source bioinformatics platform for genomic and biomedical data. User can Store | Organize | Compute | Share the data for free.
github.com - A flexible framework for rapid genome analysis and interpretation
C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth...
www.khanacademy.org - Topics
Displaying and describing data
Modeling distributions of data
Describing relationships in quantitative data
Designing studies
Probability
Random variables
Sampling distributions
Confidence intervals (one sample)
Significance tests...
http://itol.embl.de/ - Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize...
github.com - Simple ideogram plotting and annotation in R.
Basic usage:
Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf -or- Rscript Ideoplot.R --annotate annotations.bed
Options
--ideobed, i A bed file of reference...
journals.plos.org - To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads,...