BOL: Related items

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

Abhi — Wed, 15 May 2024 14:36:12 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

Recovery of complete genomes from metagenomes

Jit — Wed, 27 Dec 2017 00:04:55 -0600

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: http://madsalbertsen.github.io/multi-metagenome/

Digest: In silico restriction digest of complete genomes

Jit — Mon, 14 May 2018 04:02:52 -0500

This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated.

A tool for restriction digest of longuser's sequences is available.

Address of the bookmark: http://insilico.ehu.es/digest/

GTDB-Tk: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Rahul Nayak — Wed, 22 Aug 2018 03:21:01 -0500

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

GTDB-Tk is under active development and validation. Please independently confirm the GTDB-Tk predictions by manually inspecting the tree and bringing any discrepencies to our attention. Notifications about GTDB-Tk releases will be available through the ACE Twitter account (https://twitter.com/ace_uq).

Address of the bookmark: https://github.com/Ecogenomics/GTDBTk

HaploTypo: a variant-calling pipeline for phased genomes

Jit — Thu, 19 Dec 2019 07:33:40 -0600

An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome.

Availability and Implementation

HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image.

Address of the bookmark: https://github.com/gabaldonlab/haplotypo

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Jit — Mon, 18 May 2020 10:53:32 -0500

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately (see Usage).

Address of the bookmark: https://github.com/dutilh/CAT

IRscope: an online program to visualize the junction sites of chloroplast genomes

Neel — Wed, 25 Nov 2020 19:44:46 -0600

eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.

Address of the bookmark: https://sites.google.com/g.hmc.edu/empress/home

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

LEGE — Mon, 06 May 2024 06:21:10 -0500

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/

Address of the bookmark: http://synorth.genereg.net/

Tools and Method for Haplotype phasing !

Manisha Mishra — Fri, 04 Sep 2020 20:41:40 -0500

Huge amounts of genotype data are being produced with recent technological advances, both from increasingly comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methods. The vast amount of knowledge contained in these results, however, is best exploited through phased haplotypes, which classify the alleles co-located on the same chromosome. Since sequence and SNP array data normally take the form of unphased genotypes, one does not specifically observe which of the two parental chromosomes, or haplotypes, falls on a specific allele. Fortunately, new advances in both computational and laboratory methods promise improved determination of haplotype phase. Following are useful tools :

Arlequin: http://cmpg.unibe.ch/software/arlequin3/

BEAGLE: http://faculty.washington.edu/browning/beagle/beagle.html

fastPHASE: http://stephenslab.uchicago.edu/software.html

GENEHUNTER: http://linkage.rockefeller.edu/soft/gh/

The Genome Analysis Toolkit:

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

IMPUTE2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

MACH: http://www.sph.umich.edu/csg/abecasis/MACH/

MERLIN: http://www.sph.umich.edu/csg/abecasis/Merlin/

PHASE: http://stephenslab.uchicago.edu/software.html

PL-EM: http://www.people.fas.harvard.edu/~junliu/plem/

“Read-backed phasing” algorithm: http://www.broadinstitute.org/gsa/wiki/index.php/Read-backed_phasing_algorithm

SHAPE-IT: http://www.griv.org/shapeit/

Structural polymorphism analysis from NGS data

Sat, 13 Jul 2013 17:12:47 -0500

The LabEx BASC (Biodiversity, Agroecosystems, Society, Climate), a network of 13 laboratories of the Paris-Saclay Scientific Cluster, is seeking a bioinformatician to analyze Next Generation Sequencing (NGS) data analysis. In the context of a flagship project aiming at understanding and improving the adaptive capacity of agroecosystems it will be critical to establish a link between sequence variation, functional variation, gene/protein expression and phenotypic adaptation.

The successful candidate will be in charge of the detection of polymorphisms including structural variants, of the comparison of multiple and diverse genomes of a same species and of the construction of pan- and core-genomes. These challenging tasks will require bioinformatics developments and implementation of methods for accommodating the high level of repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-users through the Galaxy platform. The bioinformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements. He/she will be hosted by a bioinformatics/informatics team (7 people) (http://moulon.inra.fr/index.php/fr/equipestransversales/atelier-de-bioinformatique) which has computational facilities and expertise in NGS data analysis, and will benefit as well from national and international collaborative networks (Aplibio http://www.renabi.fr/platforms/aplibio/, Transplant http://transplantdb.eu, AMAIZING http://www.amaizing.fr/).

The position requires a doctoral degree (PhD) in bioinformatics with strong expertise in script writing (Python/Perl) and pipeline development.

Applicants should send a CV and the names of 2 referees willing to provide a letter of recommendation to joets@moulon.inra.fr.