BOL: Related items

Zombies like bacteria!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:44:15 -0500

Do you believe in Zombies stories … Hmm confused? Don’t worry there is a news for you. Scientists from the Integrated Ocean Drilling Program have announced the findings of the long-lived bacteria, reproducing only once every 10,000 years, which have been found in rocks 2.5km (1.5 miles) below the ocean floor that are as much as 100 million years old.

" the microbes exist in very low concentrations, of around 1,000 microbes in every tea spoon full of rock, compared with billions or trillions of bacteria that would typically be found in the same amount of soil at Earth's surface."

Reference:

http://www.bbc.co.uk/news/science-environment-23855436

Fancy Oneliner for Bioinformatics !!

Poonam Mahapatra — Thu, 07 Jul 2016 12:05:50 -0500

This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

BioStar — Mon, 17 Aug 2020 05:25:10 -0500

SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
Co-assembly of a large number of metagenomes via merging of individual metagenomes
Includes binning and bin checking, for retrieving individual genomes
The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

BioStar — Sat, 06 Jul 2024 04:29:16 -0500

Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
Co-assembly of a large number of metagenomes via merging of individual metagenomes
Includes binning and bin checking, for retrieving individual genomes
The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

Bambus

Jit — Tue, 16 Aug 2016 08:09:15 -0500

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Home Page:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

Coordinator of Bioinformatics Core Facility-Robert Koch Institute Berlin

Thu, 30 Jan 2020 07:01:45 -0600

We are offering the following position in unit MF 1 "Bioinformatics" of department MF "Methodology and Research Infrastructure" for a

Coordinator of our Bioinformatics Core Facility (all genders)

(salary dependent on qualifications and experience in accordance with public sector wage scale [TVöD] up to grade E 14).

The contract is not limited. The position will be available immediately.
https://www.researchgate.net/job/938589_Coordinator_of_our_Bioinformatics_Core_Facility_all_genders

mixtureS: a novel tool for bacterial strain reconstruction from reads

BioStar — Fri, 21 Aug 2020 08:23:19 -0500

mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS reliably identified the strains, their numbers and their abundance. Compared with three tools, mixtureS showed better performance in almost all simulated datasets and the vast majority of experimental datasets.

Availability

The source code and tool mixtureS is available at http://www.cs.ucf.edu/˜xiaoman/mixtureS/.

Address of the bookmark: http://www.cs.ucf.edu/~xiaoman/mixtureS/

SocBiN Bioinformatics 2014

Tue, 03 Sep 2013 18:50:20 -0500

14th annual conference in Bioinformatics

Date : June 10-13

Organizers: The Society for Bioinformatics in Northern European countries (SocBiN) and the Norwegian Bioinformatics Platform / ELIXIR.NO

Venue: Department of Informatics, University of Oslo, Norway

Topics:
Tools and technologies for integrative bioinformatics
Metagenomics
Comparative genomics and phylogeny
Post-ENCODE bioinformatics
Gene regulation
Cancer genomes
Marine genomics

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Jit — Wed, 14 Nov 2018 04:50:27 -0600

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8.

https://academic.oup.com/bioinformatics/article/31/10/1674/177884

Address of the bookmark: https://github.com/voutcn/megahit

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

Jit — Wed, 13 Jan 2021 19:29:32 -0600

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets. It reduces redundancies in multiple discoveries of the same gene and resolves conflicting gene predictions on the same strand. MetaEuk is GPL-licensed open source software that is implemented in C++ and available for Linux and macOS. The software is designed to run on multiple cores.

Address of the bookmark: https://github.com/soedinglab/metaeuk