BOL: Related items

jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

Abhimanyu Singh — Fri, 26 Jul 2019 00:58:12 -0500

jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

Jit — Fri, 24 Jan 2020 04:09:15 -0600

MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. MitoZ is available from https://github.com/linzhi2013/MitoZ.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

PhD position in Translational Medicine

Sat, 15 Feb 2020 06:07:19 -0600

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-translational-medicine-129981.html?suid=1b510358c7578e8f75cf04a464fc21a404a574ca

Essential experience / qualifications:
Master / Diploma in Biology, Biochemistry, Molecular Medicine or similar; solid knowledge of molecular and cell biological techniques; good English knowledge

Applications:
Please send your application (including CV, letter of motivation, contact information of two references, and list of publication) by 13.03.2020 at the latest to:

Universitätsklinikum Erlangen
Chirurgische Klinik
Translational Research Center
Prof. Dr. rer. nat. Michael Stürzl
Schwabachanlage 12
91054 Erlangen
E-Mail: michael.stuerzl@uk-erlangen.de

McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data

BioStar — Tue, 27 Oct 2020 00:21:18 -0500

an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae.

Address of the bookmark: https://github.com/bergmanlab/mcclintock

Figeno: Tool for plotting sequencing data along genomic coordinates.

LEGE — Tue, 17 Sep 2024 02:28:15 -0500

Tool for plotting sequencing data along genomic coordinates.

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

Address of the bookmark: https://github.com/CompEpigen/figeno

Corona Virus Literature !

Abhi — Sun, 12 Dec 2021 23:30:56 -0600

LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 201482 (and growing) relevant articles in PubMed. The articles are updated daily and are further categorized by different research topics (e.g. Long Covid) and geographic locations for improved access. You can learn more at Chen et al. Nature (2020) or our FAQ, and download our data here.

https://www.ncbi.nlm.nih.gov/research/coronavirus/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/research/coronavirus/

CLgenomics

Radha Agarkar — Fri, 03 Mar 2017 09:57:28 -0600

CLgenomics is a standalone desktop software specifically designed for bacterial genome analysis. This program has a powerful multi-genome browser, which enables rapid and responsive exploration of bacterial genomes.

To use CLgenomics, individual genome data (genome sequences + annotation details) are compiled and saved in a specially formatted file called CLG (ChunLab Genomics). Each CLG file corresponds with one bacterial genome. If multiple genomes are being considered and compared, multiple CLG files are needed. ChunLab offers >40,000 CLG files of publicly available Bacterial and Archaeal genomes.

Address of the bookmark: https://chunlab.wordpress.com/clgenomics-software/

KEGG Mapper – Reconstruct Pathway

Abhimanyu Singh — Wed, 12 Dec 2018 09:14:29 -0600

Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multiple organisms) annotated with KEGG Orthology (KO) identifiers or K numbers. Each line of the gene list contains the user-defined gene identifier followed by, if any, the assigned K number. The mapping is performed through the K numbers against the KEGG reference pathways.

Address of the bookmark: https://www.kegg.jp/kegg/tool/map_pathway.html

Proksee

LEGE — Wed, 27 Mar 2024 11:11:54 -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.

Please Cite the Following

Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, Graham M, Van Domselaar G, and Stothard P

Proksee: in-depth characterization and visualization of bacterial genomes

Nucleic Acids Research, 2023, gkad326, https://doi.org/10.1093/nar/gkad326

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

Aurora: A New Detective for Bacterial Genomes

BioStar — Fri, 21 Aug 2026 11:31:00 -0500

Imagine trying to solve a mystery with thousands of clues—but some of the clues are labelled incorrectly.

That is the challenge researchers face when studying how bacteria adapt to different environments. A bacterial gene may appear to be linked to a particular habitat, when the real reason is simply that closely related bacteria happen to live there.

In their 2025 Genome Biology paper, Bujdoš, Walter, and O’Toole introduce aurora, a machine-learning tool designed to tackle this problem.

Aurora identifies potentially mislabeled or unusual bacterial strains before performing genome-wide association studies (GWAS). By cleaning up the dataset and accounting for bacterial evolutionary relationships, it can help researchers find genetic features that are more genuinely connected to habitat adaptation.

The researchers tested aurora using simulated and real bacterial datasets and found that it could recover important genetic associations even when datasets contained misleading labels.

The bigger lesson is simple: better biological discoveries often begin with better data.

Aurora gives researchers a new way to separate real genetic clues from misleading ones—and could help us better understand how bacteria adapt, survive, and evolve in the environments they call home.

Based on Bujdoš et al., “aurora: a machine learning GWAS tool for analyzing microbial habitat adaptation,” Genome Biology (2025).[Read the original paper](https://link.springer.com/article/10.1186/s13059-025-03524-7?)