A recent study by Webster and Chapman introduces Buscogeny (https://github.com/Jwebster89/Buscogeny), an open-source bioinformatics pipeline designed to make this process easier. The tool uses BUSCO (Benchmarking Universal Single-Copy Orthologs), which identifies conserved genes that are expected to occur as single copies in particular groups of organisms. These genes act like evolutionary landmarks, allowing researchers to compare genomes and investigate their relationships.

Buscogeny brings several steps of phylogenomic analysis into one workflow. It identifies BUSCO genes, extracts and aligns their sequences, removes unreliable regions, combines information from multiple genes, and uses the resulting data to construct a phylogenetic tree. It also provides quality-control information, helping researchers identify genomes that may be too incomplete for reliable analysis.

The authors demonstrate the usefulness of Buscogeny with bacterial and fungal genomes, including Alternaria. This is particularly valuable because fungal genomes can vary greatly in quality and annotation. Ultimately, Buscogeny helps transform massive amounts of genomic data into an understandable evolutionary story. Each DNA sequence becomes a clue, each conserved gene becomes a landmark, and together these clues reveal a picture of how life is connected.

More at https://link.springer.com/article/10.1007/s10123-025-00752-6?

Address of the bookmark: http://denbi-metagenomics-workshop.readthedocs.io/en/latest/index.html

Address of the bookmark: http://disco.omicsbio.org/

This bookmark is created to provide NGS online books links.

Address of the bookmark: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version

TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. 
Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.

https://github.com/Generade-nl/TULIP

Address of the bookmark: https://github.com/Generade-nl/TULIP

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

National Bioinformatics Infrastructure Sweden (NBIS) (nbis.se) plays an important role in advancing life science research in Sweden by providing expert support and developing cutting-edge bioinformatics infrastructure. Operating as a truly national initiative, NBIS employs more than 120 bioinformaticians, system developers, and data stewards across multiple locations in Sweden. It serves as the bioinformatics platform at SciLifeLab, a national resource that facilitates research in molecular biosciences by offering access to state-of-the-art technologies and technical expertise. With strong ties to data-producing facilities and ongoing collaborations with leading research groups, NBIS is ideally positioned to support world-class bioinformatics analyses. Furthermore, NBIS is the Swedish node in ELIXIR, the European infrastructure for biological information.

NBIS is seeking an experienced bioinformatician to support both Swedish and international projects. As part of our dynamic team, you will work closely with researchers to process large-scale biological data and contribute to advancing our data analysis infrastructure. Strong problem-solving skills, attention to detail, and the ability to troubleshoot complex bioinformatics pipelines are essential for success in this role. Flexibility and a willingness to learn are also important, as NBIS continually adapts to meet the evolving needs of the Swedish research community.

More at https://www.uu.se/en/about-uu/join-us/jobs-and-vacancies/job-details?query=778701

• Assembly of nanopore reads using Canu.
• Polish canu contigs using racon (optional).
• Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem.
• Perform correction of contigs using pilon and the Illumina dataset.

Address of the bookmark: https://github.com/nanoporetech/ont-assembly-polish

1. Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
2. Reducing/removing reference bias as compared to mapping based approaches.

The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.

https://ibest.github.io/ARC/

Address of the bookmark: https://ibest.github.io/ARC/

Address of the bookmark: https://github.com/carolzhou/multiPhATE