Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087/

https://nxrepair.readthedocs.io/en/latest/tutorial.html

nxrepair aligned_matepairs.bam assemblyfasta.fasta error_locations.csv new_fasta.fasta

Address of the bookmark: https://github.com/rebeccaroisin/nxrepair

Address of the bookmark: http://pacb.com/blog/the-hifi-difference-true-long-reads-vs-synthetic-long-reads/

Metagenomic simulators are a way of dealing with this issue; they produce artificial sequencing datasets in which both the composition of the microorganisms and the expected results are known. Researchers can then test a pipeline on such a controlled dataset and see precisely how well it functions. However, as metagenomic studies have become larger, more diverse, and more complex, simply generating artificial reads is no longer sufficient. The simulators now have to replicate community variation, sequencing errors, different sequencing platforms, massive data volumes, and even laboratory-based biases.

MIDASim (2024) was designed with a particular emphasis on microbial community dynamics. Unlike previous tools which regarded each simulated sample as individual, MIDASim is able to efficiently generate realistic multi-sample microbiome datasets, covering the cases where changes over time are being tracked. This feature is particularly useful when investigating how microbial communities vary between people, different experimental setups, or at various times. By overcoming the computational limitations of earlier simulation methods, MIDASim has made it easier to carry out large and complex microbiome simulation studies.

A major challenge is scale. Since modern metagenomic projects can involve millions or even billions of sequencing reads, generating such large synthetic datasets can become a significant computational problem. In order to tackle this issue, Izzy (2025) was developed. As a high-throughput metagenomic read simulator, Izzy is designed with speed in mind while still reproducing the typical patterns of sequencing errors. The people who developed it stated that it can be as much as 60 times faster than earlier tools, which makes large-scale simulations far more practical. Now, researchers can begin to ask not how long a simulation will take but rather what size dataset they want to test.

At the same time, the sequencing technology became more diverse. Researchers were not any longer restricted to using Illumina short reads since Oxford Nanopore and PacBio long-read sequencing also became important in the field of metagenomic research. In order to address these new requirements, MeSS (Metagenomic Sequence Simulator, 2025) was developed. The programme is based on a Snakemake framework and is therefore compatible with the Illumina, Oxford Nanopore and PacBio platforms. MeSS has also been designed to operate efficiently and to use less memory than earlier tools; it provides ready-made templates for the microbiomes of different sites in the human body, thus giving researchers a simple means of beginning to generate realistic simulated communities.

The simulation problem became even more specialized. Suppose that sequencing is not based on uniform sampling of DNA? In the case of targeted sequencing and hybridization-capture experiments, particular sequences are deliberately enriched, and the probability of capturing a target depends on both the probe and the target sequence. A standard model based on uniform sampling might fail to take into account this important feature of real experiments. That is why RAmpSim has been designed specifically to handle simulations for capture-based and targeted sequencing. Instead of depending solely on the assumption of uniform sampling, it includes a thermodynamic nearest-neighbor energy model to represent probe–target interactions and sequence-dependent enrichment. As a result, it is especially suitable for applications such as hybridization capture in metagenomics, where the efficiency of recovering a sequence can depend strongly on how it relates to the capture probes. RAmpSim thus reflects a wider trend towards simulations that aim not only to reproduce sequencing output but also key aspects of the experimental process itself.

MIDASim, Izzy, MeSS and RAmpSim all demonstrate how fast metagenomic simulation is evolving. MIDASim is able to deal with realistic variation within a large number of and changing microbial communities. Izzy overcomes the problem of generating very large datasets. MeSS provides support for a number of sequencing technologies in an efficient and repeatable manner. RAmpSim increases the experimental realism for capture-based sequencing. Although each of these tools addresses a separate issue, they all contribute to advancing the field.

Modern metagenomic simulation therefore aims not only at producing artificial FASTQ files. Researchers nowadays desire simulated datasets that reflect community changes, incorporate the characteristics of the sequencing platform, include real error patterns, take into account computational scale, and account for experimental biases. As metagenomic workflows become more advanced, the simulators have to keep up with this development. The tools are now going beyond that of simple data generators; they produce controlled versions of complex metagenomic experiments and thus provide researchers with something that ordinary sequencing data seldom does: a dataset in which the answer is known before any analysis takes place.

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/

• New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
• New export function for BAM/cSRA coverage graphs (Tutorial)
• New export function for alignments GFF3 format ((Tutorial))
• Tree View: implemented new export mode based on selections (tutorial coming)
• Tree View: added support for distance based circular trees
• Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
• Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)

http://gkno.me/how-to/install.html

http://gkno.me/software.html

Address of the bookmark: http://gkno.me/

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Address of the bookmark: http://darlinglab.org/mauve/mauve.html

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

BBSplit is a tool that bins reads by mapping to multiple references simultaneously, using BBMap. The reads go to the bin of the reference they map to best. There are also disambiguation options, such that reads that map to multiple references can be binned with all of them, none of them, one of them, or put in a special "ambiguous" file for each of them. Paired reads will always be kept together.

For example, if you had a library of something that was contaminated with e.coli and salmonella, you could do this:

bbsplit.sh in=reads.fq ref=ecoli.fa,salmonella.fa basename=out_%.fq outu=clean.fq int=t

This will produce 3 output files:
out_ecoli.fq (ecoli reads)
out_salmonella.fq (salmonella reads)
clean.fq (unmapped reads)

In this case, "int=t" means that the input file is paired and interleaved. For single-end reads you would leave that out. For paired reads in 2 files, you would do this:
bbsplit.sh in1=reads1.fq in2=reads2.fq ref=ecoli.fa,salmonella.fa basename=out_%.fq outu1=clean1.fq outu2=clean2.fq

BBSplit is available here:
https://sourceforge.net/projects/bbmap/

The sensitivity can be raised to be equivalent to BBMap with these flags: "minratio=0.56 minhits=1 maxindel=16000"