Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

https://pubmed.ncbi.nlm.nih.gov/25725497/

Address of the bookmark: https://github.com/sanger-pathogens/iva

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?

Address of the bookmark: https://github.com/alastair-droop/fqtools

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

Progressive Cactus is a whole-genome alignment package.

Requirements

• git
• gcc 4.2 or newer
• python 2.7
• wget
• 64bit processor and build environment
• 150GB+ of memory on at least one machine when aligning mammal-sized genomes; less memory is needed for smaller genomes.
• Parasol or SGE for cluster support.
• 750M disk space

Instructions

IMPORTANT NOTE: Progressive Cactus does not presently support installation into paths that contain spaces. Until this is resolved, you can use a softlink as a workaround: ln -s "path with spaces" "installation path without spaces"

In the parent directory of where you want Progressive Cactus installed:

git clone git://github.com/glennhickey/progressiveCactus.git
cd progressiveCactus
git pull
git submodule update --init
make

It is also convenient to add the location of progressiveCactus/bin to your PATH environment variable. In order to run the included tools (ex hal2maf) in the submodules/ directory structure, first source progressiveCactus/environment to load the installed environment.

If any errors occur during the build process, you are unlikely to be able to use the tool. Please submit a GitHub issue so we can help out: not only will you help yourself, but others who wish to use the tool as well.

Note that all dependencies are also built and included in the submodules/ directory. This increases the size and build time but greatly simplifies installation and version management. The installation does not create or modify any files outside the progressiveCactus/ directory.

Address of the bookmark: https://github.com/glennhickey/progressiveCactus

http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/

Address of the bookmark: http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/

TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

• The latest TMAP is unsupported. To use a supported version, please see the TMAP version associated with a Torrent Suite release below.

• Get the latest source code:

  git clone git://github.com/iontorrent/TMAP.git
   cd TMAP
   git submodule init
   git submodule update

https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

Address of the bookmark: https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

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

Address of the bookmark: http://schatzlab.cshl.edu/data/nanocorr/