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

BRIG

Jit — Thu, 16 Feb 2017 13:14:25 -0600

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page:http://sourceforge.net/tracker/?group_id=328245.

Features:

Images show similarity between a central reference sequence and other sequences as concentric rings.
BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

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

PBSuite: Software for Long-Read Sequencing Data from PacBio

Jit — Mon, 27 Feb 2017 09:54:47 -0600

PBJelly - the genome upgrading tool.
PBHoney - the structural variation discovery tool

Both are contained within the PBSuite code found in downloads.

----- PBJelly -----
Read The Paper
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.

----- PBHoney -----
Read The Paper
http://www.biomedcentral.com/1471-2105/15/180/abstract

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Address of the bookmark: https://sourceforge.net/projects/pb-jelly/

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

SSPACE

Jit — Fri, 05 May 2017 05:42:15 -0500

SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format.

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Jit — Wed, 19 Apr 2017 10:09:51 -0500

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

Address of the bookmark: https://github.com/yechengxi/DBG2OLC

MeDuSa: a multi-draft based scaffolder

Abhimanyu Singh — Wed, 14 Feb 2018 02:49:00 -0600

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries.

Address of the bookmark: https://github.com/combogenomics/medusa

India and Germany to begin joint research in the area of 'Bioinformatics in Health Research'

Rahul Nayak — Wed, 17 Jan 2018 14:10:36 -0600

To facilitate bilateral cooperation in biotechnology between the scientific communities of India and Germany, the Department of Biotechnology (DBT) will soon begin collaborative research in the identified priority area of 'Bioinformatics in Health Research' under the programme of Indo-German Cooperation in Health Research.

The purpose of the programme is to stimulate new collaborations, e.g. the preparation of joint projects under national funding programmes. The programme facilitates bilateral cooperation in biotechnology between the scientific communities of India and Germany by way of joint research projects which will encompass bilateral workshops/seminar and exchange visits of scientists.

The programme is being implemented within the agreement of Indo-German cooperation in S&T of 1974, under which the Department of Biotechnology, Government of India and Forschungszentrum Julich BMBH (FZJ), Federal Republic of Germany, have agreed for cooperative programme in biotechnology.

DBT of the Ministry of Science & Technology, Government of India and the Project Management Agency at the German Aerospace Center (DLR-PT, European and International Cooperation), Bonn are the nodal implementing agencies from the Indian and German side respectively.

Through this programme, it is expected that the funded cooperation enables the partners to develop applicable scientific results which can be published and/ or could be commercialised and may lead to formation of joint ventures. All publications, patents coming out of these projects, need to be jointly authored by both Indian and German scientists. All necessary approvals like ethical clearance, HMSC approval from Indian point of view as well as EU, if applicable, from German point of view, e.g. before conducting animal experimentation if any needs to be obtained by PIs before undertaking the project.

Now, both the nodal agencies have invited research proposals in identified priority area of 'Bioinformatics in Health Research' from eligible scientists. Joint research projects are required to be submitted to both the nodal agencies by 15 January 2018. Scientists/faculty members working in regular capacity in universities, national R&D laboratories/institutes and private R&D institutes can be part of this joint research programme. For the private sector, partners from all kind of private sectors are eligible, but financing is limited. For Indian scientists from the private sector, only local hospitality in Germany as part of the exchange visit is available from the German side. For German scientists from the private sector, only travel costs are available for small and medium size enterprises (for definition of SME ref. to 2003/361/EC) as well as local hospitality in India will be borne by themselves.

Researcher in computer science/biology

Mon, 15 Jul 2013 18:38:40 -0500

Researcher in Computer Science at the Computational Biology Unit - temporary employment

The Department of Informatics is a vacant position as a researcher in computer science, related to Computational Biology Unit (CBU), for 3 years.

The position is part of CBU Service Group and will focus on bioinformatic analysis project and especially the analysis of high-throughput data, including NGS (sequencing), and proteomics data.

The successful candidate will be part of the Norwegian bioinformatics platform's national helpdesk within the project ELIXIR.NO

Applicants must hold a PhD in a relevant subject such as computer science, mathematics, molecular biology and also possess expertise and experience in bioinformatics statistics and analysis of data from high-throughput molecular experiment.

Basic programming or scripting skills are required. Experience in Python, R, Perl, Linux-based operating systems and moreover knowledge of databases and web programming will be a strength for applicants.

We expect enthusiasm and independence and moreover the ability to work in an interdisciplinary team environment.

Good knowledge of English is required.

Salaries start at level 57 (code 1109/LR 24.1) by appointment. Further promotion occurs after
service seniority in the position (at grade 57-65). Of particularly highly qualified applicants may be considered a higher salary.

Further information about the position is available from the chair of the CBU,
Professor Inge Jonassen, e-mail: Inge.Jonassen @ ii.uib.no

The successful applicant must comply with the guidelines that apply at any given time the position.

State employment shall as far as possible reflect the diversity of the population. It is therefore an objective to achieve a balanced age and sex composition and the recruitment of persons with immigrant backgrounds. Persons with immigrant background are requested to apply for the position.

Women are particularly encouraged to apply. If the experts find that several applicants have approximately equivalent qualifications, the rules on equal in the Personnel Regulations for Academic Positions will be applied.

University of Bergen applies the principles of public openness when recruiting staff to scientific positions.

Information about the applicant may be made public even though the applicant has requested not to be named in the list of applicants. If the request does not host admitted to the result, the applicant shall be notified of this.

Send application, CV, certificates, diplomas, undergraduate work and a list of publications (list of publications) online by clicking on https://www.jobbnorge.no/jobbsoknet/login.aspx?returnurl=/jobbsoknet/jobapplication.aspx?jobid=95196

You need to upload certified translations into English or a Scandinavian language of appendices, such as diplomas and transcripts.

Applications sent by email to individuals at the institute will not be considered.

Deadline: 9 August 2013