BOL: Related items

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

TRITEX sequence assembly pipeline for Triticeae genomes

Jit — Tue, 20 Aug 2019 09:47:14 -0500

The pipeline is open-source and hosted in a public Bitbucket repository.

TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a BAC-by-BAC assembly. It has never been tested and is not expected to work on heterozygous or autopolyploid genomes.

A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium data.

Address of the bookmark: https://tritexassembly.bitbucket.io/

Kevler: Reference-free variant discovery in large eukaryotic genomes

Jit — Tue, 28 Jan 2020 03:21:53 -0600

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model.

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

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/

TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes

LEGE — Fri, 14 Feb 2025 10:53:48 -0600

This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK) Gatersleben.

Address of the bookmark: https://tritexassembly.bitbucket.io/

AGORA: Algorithm for Gene Order Reconstruction in Ancestors

Jit — Mon, 28 Feb 2022 23:26:21 -0600

AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” and was developed by Matthieu Muffato in the DYOGEN Laboratory at the École normale supérieure in Paris in 2008.

    // | |     //   ) )  //   ) ) //   ) )  // | |
   //__| |    //        //   / / //___/ /  //__| |
  / ___  |   //  ____  //   / / / ___ (   / ___  |
 //    | |  //    / / //   / / //   | |  //    | |
//     | | ((____/ / ((___/ / //    | | //     | |

AGORA is used to generate ancestral genomes for the Genomicus online server for gene order comparison, and has been in constant use in the group since.

Address of the bookmark: https://github.com/DyogenIBENS/Agora

pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction

LEGE — Wed, 21 Feb 2024 06:19:41 -0600

ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

FGENESH - Program for predicting multiple genes in genomic DNA sequences

BioStar — Thu, 20 Dec 2018 11:55:08 -0600

FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff et al. (2002) Science 296:79).

Address of the bookmark: http://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind