BOL: Related items

GAM-NGS: genomic assemblies merger for next generation sequencing

Jit — Mon, 19 Dec 2016 06:07:05 -0600

GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus (called blocks) are identified through reads' alignments and stored in a weightedgraph. The merging phase is carried out with the help of this weighted graph that allows an optimal resolution of local problematic regions.

Address of the bookmark: https://github.com/vice87/gam-ngs

Genome Assembly Tutorial

Abhimanyu Singh — Tue, 20 Dec 2016 07:56:01 -0600

If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard to assemble using overlap-consensus-layout approach. De Bruijn graph-based assembly approach was originally proposed to handle the assembly of repetitive regions better.

More at http://www.homolog.us/Tutorials/index.php?p=1.4&s=1

Address of the bookmark: http://www.homolog.us/Tutorials/index.php?p=1.4&s=1

GenomeRing: alignment visualization based on SuperGenome coordinates

Neel — Wed, 18 Jan 2017 10:24:10 -0600

The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

More at https://academic.oup.com/bioinformatics/article/28/12/i7/268598/GenomeRing-alignment-visualization-based-on

Address of the bookmark: http://it.informatik.uni-tuebingen.de/?page_id=185

HivePlot

Jit — Thu, 16 Feb 2017 11:39:34 -0600

The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links. Simple and interpretable.

The purpose of the hive plot is to establish a new baseline for visualization of large networks — a method that is both general and tunable and useful as a starting point in visually exploring network structure.

More at http://www.hiveplot.com/

Address of the bookmark: http://www.hiveplot.com/

DIAL

Abhimanyu Singh — Wed, 01 Mar 2017 08:42:28 -0600

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management.

http://www.bx.psu.edu/~ratan/

Address of the bookmark: http://www.bx.psu.edu/miller_lab/

splitbam: splits a BAM by chromosomes

Jit — Tue, 28 Feb 2017 09:01:28 -0600

splitbam splits a BAM by chromosomes.

Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash.

Usage

java -jar splitbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin)

Options

-h help; This screen.
-R (indexed reference file) REQUIRED.
-u (unmapped chromosome name): default:Unmapped
-e | --empty : generate EMPTY bams for chromosome having no read mapped
-m | --mock : if option '-e', add a mock pair of sam records to the empty bam
-p (output file/bam pattern) REQUIRED. MUST contain __CHROM__ and end with .bam
-s assume input is sorted.
-x | --index create index.
-t | --tmp (dir) tmp file directory
-G (file) chrom-group file (see below)

Address of the bookmark: https://code.google.com/archive/p/jvarkit/wikis/SplitBam.wiki

Computer Theory & Genetics: George Chao at TEDxUMNSalon

Thu, 15 Aug 2013 22:08:10 -0500

George Chao is an undergraduate senior studying Genetics and Computer Science at the University of Minnesota. Having started genetics research as soon as he entered the university, he has worked in labs spanning multiple disciplines as well as in Japan. Some of these researches include developmental genetics in Drosophila, computational techniques for analyzing protein interactions, and helping with the development of algorithms to analyze motion capture data of patients with neck pain. During this time, George steadily developed a fascination with the field of bioinformatics, the study of using computational techniques to learn from genetic data. He would like to go into a career of research into the application of bioinformatics in various fields. ---- The individuals involved with TEDxUMN have a passion for bringing together the great thinkers at the University of Minnesota and giving them the opportunity to share their ideas worth spreading and to discuss our shared future. We provide these great people the opportunity to share these ideas on a global stage and with an incredibly diverse audience. We believe in the power of ideas to change attitudes, lives and ultimately the world. Check out TEDxUMN at http://www.TEDxUMN.com/ In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience. At a TEDx event, TEDTalks video and live speakers combine to spark deep discussion and connection in a small group. These local, self-organized events are branded TEDx, where x = independently organized TED event. The TED Conference provides general guidance for the TEDx program, but individual TEDx events are self-organized.* (*Subject to certain rules and regulations)

CLgenomics

Radha Agarkar — Fri, 03 Mar 2017 09:57:28 -0600

CLgenomics is a standalone desktop software specifically designed for bacterial genome analysis. This program has a powerful multi-genome browser, which enables rapid and responsive exploration of bacterial genomes.

To use CLgenomics, individual genome data (genome sequences + annotation details) are compiled and saved in a specially formatted file called CLG (ChunLab Genomics). Each CLG file corresponds with one bacterial genome. If multiple genomes are being considered and compared, multiple CLG files are needed. ChunLab offers >40,000 CLG files of publicly available Bacterial and Archaeal genomes.

Address of the bookmark: https://chunlab.wordpress.com/clgenomics-software/

MaxBin: software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

Jit — Mon, 06 Mar 2017 04:03:38 -0600

MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page.

Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin after the binning process is finished.

https://academic.oup.com/bioinformatics/article/32/4/605/1744462/MaxBin-2-0-an-automated-binning-algorithm-to

The most recent version of MaxBin is 2.2, which supports the analysis of coassemblies of multiple samples. It is available at this JBEI downloads sites as well as MaxBin and MaxBin 2.0 sourceforge sites.

Address of the bookmark: http://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html

GroopM: Metagenomic binning toolset

Jit — Tue, 07 Mar 2017 08:59:45 -0600

GroopM is a metagenomic binning toolset. It leverages spatio-temoral
dynamics (differential coverage) to accurately (and almost automatically)
extract population genomes from multi-sample metagenomic datasets.

GroopM is largely parameter-free. Use: groopm -h for more info.

For installation and usage instructions see : http://ecogenomics.github.io/GroopM/

Address of the bookmark: https://github.com/ecogenomics/GroopM