BOL: Related items

Mitochondrial genome assembly tools !

Abhi — Wed, 06 Sep 2023 00:37:18 -0500

Mitochondrial genome assembly tools are specialized software and algorithms designed to accurately reconstruct the mitochondrial genome (mitogenome) from sequencing data, typically obtained through techniques like next-generation sequencing (NGS). The mitochondrial genome is relatively small compared to the nuclear genome, making it an ideal target for assembly. Here are some commonly used mitochondrial genome assembly tools:

MitoFinder: Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

MITObim: MITObim is a tool specifically developed for the iterative assembly of mitochondrial genomes. It starts with a reference mitogenome and iteratively refines the assembly using the read data.

MITOS: MITOS is a web-based platform that provides a pipeline for annotating mitochondrial genomes. It integrates multiple software tools for assembly, annotation, and visualization of mitogenomes.

MIRA: MIRA (Mimicking Intelligent Read Assembly) is a versatile genome assembly tool that can be used for mitochondrial genome assembly. It supports various sequencing technologies and allows for reference-based or de novo assembly.

NOVOPlasty: NOVOPlasty is a user-friendly tool designed for de novo assembly of organelle genomes, including mitochondria. It utilizes a seed-and-extend algorithm and is suitable for both short-read and long-read data.

MITOS2: MITOS2 is an updated version of the MITOS pipeline, which automates the annotation of mitochondrial genomes. It provides improved accuracy and additional features for mitochondrial genome analysis.

GetOrganelle: While primarily designed for chloroplast genome assembly, GetOrganelle can also be used for mitochondrial genome assembly. It is particularly useful for dealing with high-throughput sequencing data.

SPAdes: SPAdes (St. Petersburg genome assembler) is a versatile genome assembly tool that can be employed for mitochondrial genome assembly, especially when dealing with complex datasets that may contain nuclear mitochondrial DNA sequences (numts).

IDBA-UD: IDBA-UD (Iterative De Bruijn Graph De Novo Assembler) is another de novo assembly tool that can be used for mitochondrial genome assembly, especially in cases with relatively low coverage.

Velvet: Velvet is a de novo assembly tool that can be applied to mitochondrial genome assembly, especially when working with short-read data.

When selecting a mitochondrial genome assembly tool, it's important to consider the specific characteristics of your sequencing data, such as read length and coverage, as well as the complexity of the mitochondrial genome. Additionally, some tools are better suited for specific organisms or research objectives, so choosing the right tool will depend on your particular project requirements.

nf-core/mag v5: Advancing Genome-Resolved Metagenomics

LEGE — Sat, 12 Sep 2026 20:27:51 -0500

Metagenomics is rapidly moving beyond short-read sequencing. With the increasing adoption of long-read technologies, researchers can generate more contiguous assemblies—but converting these reads into reliable metagenome-assembled genomes (MAGs) remains computationally challenging.

nf-core/mag v5 (https://github.com/nf-core/mag) addresses this challenge by extending its reproducible Nextflow-based workflow for modern genome-resolved metagenomics.

A key addition is support for long-read-only metagenomic assembly and bin refinement, enabling long-read data to be processed through an integrated workflow. The release also introduces five additional binning tools, providing complementary strategies for recovering genomes from complex microbial communities.

The workflow has also expanded beyond conventional bacterial and archaeal MAGs, with improved classification of viruses and eukaryotes, together with enhanced genome-quality assessment.

Conceptually, the workflow brings together:

Reads → QC → Assembly → Binning → Bin refinement → Taxonomic classification → MAG quality assessment

The real strength of nf-core/mag is not any single algorithm, but the integration and reproducibility of multiple tools within a standardized workflow. This is particularly important for large-scale metagenomic studies where software versions, parameters, databases and computational environments can strongly influence results.

After seven years of development involving multiple curator teams and the wider nf-core community, v5 demonstrates how community-driven workflow development can keep metagenomic analysis aligned with rapidly evolving sequencing technologies.

The future of genome-resolved metagenomics is not simply longer reads—it is better integration of assembly, binning, refinement and quality control within reproducible computational workflows.

Read the full paper in Bioinformatics https://academic.oup.com/bioinformatics/article/42/9/btag628/8770536?

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

PAired-eND Assembler for DNA sequences

Neel — Wed, 06 Apr 2016 05:25:34 -0500

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

More at https://github.com/neufeld/pandaseq

Address of the bookmark: https://github.com/neufeld/pandaseq

REAPR: a universal tool for genome assembly evaluation

Jitendra Prajapati — Wed, 06 Apr 2016 18:26:31 -0500

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.

http://www.sanger.ac.uk/science/tools/reapr

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-5-r47

BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

Anjana — Tue, 10 May 2016 07:46:24 -0500

High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures like N50.
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of Benchmarking Universal Single-Copy Orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria.
These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.
BUSCO assessments offer intuitive metrics, based on evolutionarily informed expectations of gene content from hundreds of species, to gauge completeness of rapidly accumulating genomic data and satisfy an Iberian's quest for quality - "Busco calidad/qualidade".

Address of the bookmark: http://busco.ezlab.org/

Pollard Lab

Fri, 25 Sep 2020 20:20:50 -0500

We are a bioinformatics research lab focused on developing novel methods and using them to study genome evolution, organization, and regulation. Our mission is to decode biomedical knowledge that is missed without rigorous statistical approaches.

http://docpollard.org/

Tools

http://docpollard.org/resources/software/

Platanus

Jit — Fri, 13 May 2016 05:12:40 -0500

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of
highly heterozygous diploids from massively parallel shotgun sequencing data.

The latest version is 1.2.4.

To cite Platanus, please use the following:

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113. [abstract | full text]

Address of the bookmark: http://platanus.bio.titech.ac.jp/

Bambus

Jit — Tue, 16 Aug 2016 08:09:15 -0500

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Home Page:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

NGS teaching material

Jit — Wed, 05 Apr 2017 04:29:06 -0500

High throughput sequencing (HTS) technologies are being applied to a wide range of important topics in biology. However, the analyses of non-model organisms, for which little previous sequence information is available, pose specific problems. This course addresses the specific strengths and weaknesses of alternative HTS technologies, the computational resources needed for HTS, and how to analyze non-model species using HTS. The course consists of a practical training module, HTS bioinformatics training, and lecturing/seminars of HTS approaches specifically targeting non-model organisms.

Address of the bookmark: http://marinetics.org/teaching/hts/Assembly.html