<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39612?offset=1300 https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments Fri, 13 May 2016 05:25:26 -0500 https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments <![CDATA[SATSUMA : Highly sensitive whole-genome synteny alignments.]]> Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

You can find the manual here.
Download the latest source code from here.
Stable versions can also be downloaded from the Broad Institute's web site.

An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

If you use Satsuma in your research, please cite:
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

Tutorial at http://evomics.org/learning/genomics/satsuma/

Address of the bookmark: http://satsuma.sourceforge.net/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27438/hagfish-assess-an-assembly-through-creative-use-of-coverage-plots Fri, 20 May 2016 19:08:17 -0500 https://bioinformaticsonline.com/bookmarks/view/27438/hagfish-assess-an-assembly-through-creative-use-of-coverage-plots <![CDATA[Hagfish - assess an assembly through creative use of coverage plots]]> Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment.

Hagfish requires a reference sequence and a paired end re-sequencing data set. Hagfish has more power the larger the insert size of the paired end library is.

Quick links: Installation,Operation, Read mappers, Hagfish scripts, Hagfish plots

Address of the bookmark: https://github.com/mfiers/hagfish

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/27440/stampy Fri, 20 May 2016 19:13:32 -0500 https://bioinformaticsonline.com/bookmarks/view/27440/stampy <![CDATA[Stampy]]> Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions.

Address of the bookmark: http://www.well.ox.ac.uk/project-stampy

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/27461/maftools Sat, 21 May 2016 22:40:21 -0500 https://bioinformaticsonline.com/bookmarks/view/27461/maftools <![CDATA[mafTools]]> Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

Address of the bookmark: https://github.com/dentearl/mafTools

]]> Radha Agarkar