BOL: Related items

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/

mmgenome: Tools for extracting individual genomes from metagneomes

Jit — Thu, 09 Aug 2018 17:41:17 -0500

The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reproducible through the Rmarkdown format.

The mmgenome R package also facilitates effortless integration with additional data sources and hence should not be seen as "yet another binning method", but rather a package to integrate different binning strategies.

All functions in the mmgenome R package has associated documentation, check it out in R by e.g. ?mmplot.

Address of the bookmark: https://github.com/MadsAlbertsen/mmgenome

ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data

BioStar — Thu, 20 Dec 2018 12:03:32 -0600

The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes. ALLHIC pipeline contains a total of 5 steps: prune, partition, rescue, optimize and build.

Address of the bookmark: https://github.com/tangerzhang/ALLHiC/wiki

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

RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

Rahul Nayak — Fri, 01 May 2020 03:00:40 -0500

RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.

Address of the bookmark: https://github.com/AppliedBioinformatics/RefKA

PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes

BioStar — Thu, 13 Aug 2020 10:06:19 -0500

PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends on performing a all-vs-all sequence comparison, usually using BLAST, to determine homology. However, these methods are computationally expensive, requiring O(n2) resources to identify RBHs. This is problematic, as the modern deluge of sequencing data means that comparative genomics analyses could be performed on datasets of thousands of strains.

Address of the bookmark: https://github.com/ryanmelnyk/PyParanoid

Genomicus: genome browser that enables users to navigate in genomes in several dimensions

Jit — Mon, 28 Feb 2022 23:27:37 -0600

Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)


Number of extant species	200
Number of extant genes	4303993
Number of ancestral species	196
Number of ancestral genes	4624213
Number of ancestral synteny blocks	83342

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Abhi — Sat, 08 Jun 2024 16:25:08 -0500

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

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Address of the bookmark: https://bactopia.github.io/latest/

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

Abhi — Mon, 10 Jan 2022 06:32:22 -0600

This tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life.

https://www.readcube.com/articles/10.3390%2Fv9040072

Address of the bookmark: https://pubmed.ncbi.nlm.nih.gov/28387730/