BOL: Related items

CGView - Circular Genome Viewer

Jit — Mon, 19 Sep 2016 07:52:26 -0500

GView is a Java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts. For examples of some of the images GView can produce, see the Image Gallery. GView is a re-write of CGView, a circular genome viewer written by Paul Stothard. The goal of GView is to provide greater user interaction, and more flexibility in how the genome map is rendered. To aid with easily configuring the display of a genome, a style editor has been included to provide an intuitive, user-friendly graphical user interface for customizing genome maps. Styling attributes such as colours or fonts for the various map elements can be adjusted in real time. Customized styles can be saved for later use or for application to other genome maps using GView's custom file format.

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

Murasaki

Anjana — Fri, 30 Sep 2016 10:22:30 -0500

Murasaki is an anchor alignment program that is

exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes))
scalable (Arbitrarily parallelizable across multiple nodes using MPI)
memory efficient. (Even a single node with 16GB of ram can handle over 1Gbp of sequence)
unlimited by pattern length or selection
repeat tolerant

Address of the bookmark: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki

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/

gbtools: Interactive Visualization of Metagenome Bins in R

Jit — Sun, 26 Mar 2017 15:41:31 -0500

We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other.

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

DESCHRAMBLER

Jit — Thu, 29 Jun 2017 11:54:59 -0500

DESCHRAMBLER is shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools

You can find the detail of reconstructed data at http://bioinfo.konkuk.ac.kr/DESCHRAMBLER/

Address of the bookmark: https://github.com/jkimlab/DESCHRAMBLER

SALSA: A tool to scaffold long read assemblies with Hi-C

Jit — Fri, 15 Jun 2018 04:01:15 -0500

This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.261149 Link For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).

Address of the bookmark: https://github.com/machinegun/SALSA

Genome sequence-based (sub-)species delineation.

Abhimanyu Singh — Wed, 12 Dec 2018 08:31:14 -0600

The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C content.

http://ggdc.dsmz.de/ggdc_background.php#

Genome-to-Genome Distance Calculator 2.1

http://ggdc.dsmz.de/ggdc.php

Address of the bookmark: http://ggdc.dsmz.de/

Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup

Jit — Sat, 13 Apr 2019 08:55:31 -0500

Darwin-WGA, is the first hardware accelerator for whole genome alignment and accelerates the gapped filtering stage. Darwin-WGA also employs GACT-X, a novel algorithm used in the extension stage to align arbitrarily long genome sequences using a small on-chip memory, that provides better quality alignments at 2× improvement in memory and speed over the previously published GACT algorithm. Implemented on an FPGA, Darwin-WGA provides up to 24× improvement (performance/$) in WGA over iso-sensitive software.

https://stanford.edu/~yatisht/pubs/darwin-wga.pdf

Address of the bookmark: https://github.com/gsneha26/Darwin-WGA

Genome Informatics Section Lab !

Sat, 25 Jan 2020 06:38:23 -0600

Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

The Genome Informatics Section is hiring! Come join our outstanding team at the NIH’s National Human Genome Research Institute and contribute to the development of new reference genomes and computational methods for DNA sequencing and analysis. Both postdoc and PhD students positions are available. More information and application instructions follow below.

More at https://genomeinformatics.github.io/

Edanchin Lab

Thu, 19 Nov 2020 08:00:07 -0600

My main topics of interest are:

The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology
Evolution and adaptation of animals in the absence of sexual reproduction and the underlying mechanisms
Genomic signatures of adaptation to a parasitic life-style

More at https://edanchin.org/