BOL: Related items

shovill: Assemble bacterial isolate genomes from Illumina paired-end reads

BioStar — Sat, 02 Jan 2021 07:05:36 -0600

Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.

Address of the bookmark: https://github.com/tseemann/shovill

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

Jit — Sat, 18 Nov 2017 16:10:16 -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.

Address of the bookmark: http://genomicus.biologie.ens.fr/genomicus-90.01/cgi-bin/search.pl

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

Proksee: in-depth characterization and visualization of bacterial genomes

LEGE — Tue, 09 May 2023 19:38:52 -0500

Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

Address of the bookmark: https://proksee.ca/