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"

https://www.hindawi.com/journals/ijpg/2011/373875/

Address of the bookmark: https://sourceforge.net/projects/cvit/

Address of the bookmark: https://rpubs.com/Devashish13/PCAGenomics

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

Address of the bookmark: https://github.com/CompEpigen/figeno

To tackle this problem, researchers developed a new bioinformatics tool called ntSynt. It was first introduced in a 2025 study in BMC Biology titled “ntSynt: multi-genome synteny detection using minimizer graph mappings”. This tool (https://github.com/BirolLab/ntSynt) helps researcher find conserved genomic regions across several species without relying on traditional whole-genome alignments or gene annotations. Instead, ntSynt uses short DNA sequences called minimizers as landmarks. It finds minimizers shared by different genomes and maps their relationships in a graph, making it possible to spot large genomic regions that have kept a similar structure over time. The tool uses Bloom filters and graph-based mapping, which lets scientists analyze many genomes at once while saving memory and processing time.

The team tested ntSynt using both simulated data and real genomic sequences from groups like humans, chimpanzees, bonobos, gorillas, rodents, and bees. Their results showed that ntSynt can find conserved genomic regions and spot structural differences between species. In simulated tests, ntSynt identified syntenic blocks with over 97% accuracy. One standout example involved eleven bee genomes from the genus Andrena, which have a lot of variation in chromosome organization. Despite these differences, ntSynt found conserved regions covering about 85% of the smallest bee genome, completing the analysis in just 14.7 minutes and using less than 4 GB of memory. These findings highlight ntSynt’s potential for large-scale comparative genomics, where efficiency is crucial as more genomes become available.

An interesting result came up when the researchers compared primate genomes. When they looked at regions conserved between humans and other great apes, ntSynt flagged what looked like a large deletion in one gorilla genome assembly. After checking with long-read sequencing data, they found that the missing section was likely a mistake in the assembly, not a real evolutionary change. This means ntSynt can help not only with studying evolutionary relationships but also with spotting possible errors in genome assemblies. By highlighting unexpected breaks in regions that are usually conserved, the tool helps scientists tell apart true evolutionary changes from technical mistakes in reference sequences.

The importance of ntSynt becomes even clearer when we look at global projects to sequence and study Earth’s biodiversity. Projects like the Earth BioGenome Project aim to create genomic resources for many different organisms, opening up new ways to explore the history of life. But generating genomic data is just the beginning; making sense of these relationships requires powerful and scalable tools. ntSynt helps by letting researchers study chromosome evolution, conserved genome structures, and rearrangements across many species. While the tool has some limits, especially with detecting duplicated regions or analyzing very different genomes, its speed and scalability make it a valuable tool for modern comparative genomics.

The creation of ntSynt marks a significant advancement in our understanding of how genomes have evolved and become diverse over Earth's history. Since each conserved region in the genome is evidence of common ancestry and each rearrangement gives hinThe development of ntSynt is a big step forward in understanding how genomes have changed and diversified over time. Each conserved region in a genome points to shared ancestry, and each rearrangement offers clues about evolutionary events in different lineages. ntSynt helps scientists spot these patterns more easily, opening up new ways to study genome evolution across the tree of life. Evolution’s story isn’t just in the DNA sequence, but also in how those sequences are arranged and preserved over millions of years. Tools like ntSynt are helping scientists read this hidden story more clearly and reveal the deep genomic connections that link all life on Earth.

More at https://link.springer.com/article/10.1186/s12915-025-02455-w?

Address of the bookmark: http://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html

Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html.

Address of the bookmark: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp051

Address of the bookmark: https://www.niehs.nih.gov/research/resources/software/biostatistics/acana/index.cfm

Address of the bookmark: https://github.com/pratas/smash

Address of the bookmark: https://github.com/meiji-bioinf/heap