BOL: Related items

KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation

Abhimanyu Singh — Wed, 12 Dec 2018 09:16:55 -0600

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode. See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

Minipolish: A tool for Racon polishing of miniasm assemblies

BioStar — Tue, 03 Dec 2019 02:40:54 -0600

Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

Adding read depth information to contigs
Fixing sequence truncation that can occur in Racon
Adding circularising links to circular contigs if not already present (so they display better in Bandage)
'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Jit — Mon, 17 Feb 2020 05:38:46 -0600

Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.

Address of the bookmark: http://catchenlab.life.illinois.edu/chromonomer/

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

Sibelia: A comparative genomics tool

BioStar — Sat, 22 Aug 2020 02:49:00 -0500

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

More at http://bioinf.spbau.ru/sibelia

Sibelia docs http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md

Address of the bookmark: https://github.com/bioinf/Sibelia

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

Neel — Wed, 23 Jun 2021 07:54:53 -0500

LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

LEGE — Wed, 08 May 2024 07:02:55 -0500

Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

Des Higgins: Visualizing Multiple Sequence Alignments

Wed, 26 Feb 2014 00:50:08 -0600

Copyright Broad Institute, 2013. All rights reserved. Des Higgins (http://www.bioinf.ucd.ie) gives a very entertaining introduction to the visualization of multiple sequence alignment, and to his widely-used Clustal tool. He highlights the emerging challenge of managing alignments with a very large number of sequences, and presents several approaches to this challenge, including faster algorithms and abstract views of clusters of alignments. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO. For information about data visualization efforts at the Broad Institute, please visit: http://www.broadinstitute.org/node/1363/

MEDEA: Comparative Genomic Visualization with Adobe Flash

Jit — Tue, 26 Apr 2016 12:15:16 -0500

As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets.

More at http://www.broadinstitute.org/annotation/medea/

Address of the bookmark: http://www.broadinstitute.org/annotation/medea/

Anvio

Shruti Paniwala — Thu, 16 Jun 2016 18:15:41 -0500

In a nutshell

Anvi’o is an analysis and visualization platform for ‘omics data.

Please find the methods paper here: https://peerj.com/articles/1319/

Anvi’o would not have been possible without the help of many people who directly or indirectly contributed to its development. Here is the acknowledgements section of our methods paper

An analysis and visualization platform for 'omics data http://merenlab.org/projects/anvio

Paper https://peerj.com/articles/1839/

Address of the bookmark: https://github.com/meren/anvio