BOL: Related items

Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.

Jit — Wed, 20 Dec 2017 18:59:42 -0600

Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.

https://jgi.doe.gov/data-and-tools/meraculous/

https://arxiv.org/ftp/arxiv/papers/1703/1703.09852.pdf

Address of the bookmark: https://sourceforge.net/projects/meraculous20/

Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes

Jit — Fri, 02 Mar 2018 04:56:23 -0600

Horizontal gene transfer (HGT), the “non-sexual movement of genetic material between two organisms” , is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in multicellular eukaryotes. In order for a eukaryotic species to gain a gene by HGT, foreign DNA must enter the host nucleus, integrate into the genome, and in more complex organisms it must enter the sequestered germline in order to be transmitted to offspring. Once there, it must not experience strong negative selection, despite potential for genetic incompatibility with the host genome and mismatch between the niche of the donor and the host. Over the longer term, foreign DNA may become “domesticated” in the recipient genome and provide novel function.

Following are the popular tool to detect HGT in genomes:

T-REX / 3.22

HGT detection / download & compile

20525630

RANGER-DTL / 2.0

HGT detection / download binary

22689773

PhyloNet / 3.6.1

HGT detection / download binary

18662388

Jane / 4.01

HGT detection / download binary (!license!)

20181081

TREE-PUZZLE / 5.3.rc16

HGT detection / download & compile

11934758

CONSEL / 0.20

HGT detection / download

11751242

DarkHorse / 1.5 rev170

HGT detection / download & install

17274820

HGTector / 0.2.1

HGT detection / git clone

25159222

EGID / 1.0

HGT detection / download

22355228

GeneMarkS / 4.30

HGT detection / download binary (!license!)

9461475

Ranbow: a haplotype assembler for polyploid genomes

Jit — Fri, 01 Jun 2018 07:21:54 -0500

Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to improve the accuracy of variant calling results and to infer the evolutionary history of the organism´s genome. Ranbow has three main modes of function: ranbow hap: for haplotyping ranbow eval: for evaluating of the assemble haplotypes by gold standard (long) reads ranbow phylo: for the phylogenetic analysis

Address of the bookmark: https://www.molgen.mpg.de/ranbow

CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes

Jit — Wed, 24 Oct 2018 22:12:27 -0500

CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line.

CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm that identifies CSBs in large genomic datasets. The discovered CSBs are ranked according to a probabilistic score and clustered to families according to their gene content similarity.

Address of the bookmark: https://github.com/dinasv/CSBFinder

MFannot : a program for the annotation of mitochondrial and plastid genomes

Jit — Mon, 26 Aug 2019 11:47:56 -0500

MFannot is a program for the annotation of mitochondrial and plastid genomes

MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.

It makes intense use of RNA/intron detection tools including HMMER, Exonerate, Erpin and others.

http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl

Address of the bookmark: https://github.com/BFL-lab/Mfannot

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

Published a dataset of 363 genomes from approximately 92 percent of bird families

Jit — Thu, 19 Nov 2020 07:04:41 -0600

A research team published a dataset of 363 genomes from approximately 92 percent of bird families and showed the significance of sampling dense organisms for biodiversity research. The study was jointly conducted by Chinese and international institutions and museums and was led by researchers from the Kunming Institute of Zoology (KIZ) of the Chinese Academy of Sciences (CAS). Total of 267 were newly published among the 363 sequenced genomes. They were mainly taken from samples of avian tissue kept in museums around the world, enabling researchers to sequence rare and endangered birds' genomes.

Its descendants have adapted to a wide variety of ecological niches since the first bird formed more than 150 million years ago, giving rise to small, hovering hummingbirds, plunge-diving pelicans and showy paradise birds. More than 10,000 bird species live on the planet today - and now scientists are well on their way to capturing a full genetic image of that diversity.

B10K is expanding its efforts to encompass the next stage of avian classification with 363 genomes complete. The team will sequence thousands of extra genomes in this process, attempting to represent each of the approximately 2,300 bird genera.

The genomic resource is expected to provide new insights on evolutionary processes in cross-species comparative studies and assist in efforts to protect species, according to the research findings reported as a cover story in the journal Nature.

Ref at Dense sampling of bird diversity increases power of comparative genomics https://www.nature.com/articles/s41586-020-2873-9

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/

Gene Synteny Database

Jit — Fri, 16 Dec 2016 11:09:39 -0600

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.

Availability: Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus

Contact: rf.sne.eigoloib@crh

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/

DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications

Jit — Mon, 21 May 2018 11:09:02 -0500

we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tetraurelia.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205822/