http://cancerwebpa.jefferson.edu/iSeqQC/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

Address of the bookmark: https://github.com/gkumar09/iSeqQC

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim

Address of the bookmark: https://github.com/baoe/flas

It is enormous, billions of letters long. Some of those letters are easy to understand because they contain instructions for building proteins, the tiny machines that keep our cells alive.

But what if some of the most important instructions aren't in those obvious chapters?

Scientists have long suspected that the mysterious stretches of DNA between protein-coding genes may contain some of life's most interesting secrets. These regions can act like switches, telling genes when, where, and how strongly to turn on. Among them are conserved non-coding elements, or CNEs DNA sequences that have remained remarkably similar across different species.

Think of a CNE as a sentence that nature has copied into several editions of the same book.

A mouse has it.

A bird has it.

A human has it.

And despite millions of years of evolution, much of the sentence remains almost unchanged.

That conservation is a clue: this piece of DNA probably matters.

But there was a problem. Finding these hidden sentences across enormous genomes is difficult. Researchers needed to compare many genomes, identify conserved regions, and then determine which of those regions might have evolved unusually quickly in particular branches of the evolutionary tree.

Enter CNEwrap. https://github.com/YanCCscu/CNEwrap

The researchers developed CNEwrap as a streamlined toolkit capable of handling large-scale genome comparisons, conserved-element detection, and evolutionary analysis. Inside it is a new algorithm called EvoAcc, designed to identify CNEs that show accelerated evolution in specific species or lineages.

Why does that matter?

Because evolution isn't just about what stays the same.

Sometimes, the most interesting story is hidden in what changed.

Imagine that nearly every species carries the same regulatory sentence, but one lineage suddenly has several unusual edits. Perhaps those changes helped shape a new body structure, a different adaptation, or another distinctive trait.

EvoAcc is designed to help researchers find these evolutionary clues. In the study's tests, it performed particularly well in scenarios involving two or three accelerated lineages and showed improved sensitivity to insertion and deletion mutations compared with several existing approaches.

The researchers also tested CNEwrap using functional genomic regions from mammals and found that EvoAcc could recover human-specific accelerated regions while identifying some signals that other methods missed.

So the story of CNEwrap is really a story about looking beyond the obvious.

For decades, scientists have often focused on the DNA that directly encodes proteins. But the genome is more like a vast library: the protein-coding genes are the main text, while non-coding regions may contain punctuation, instructions, switches, annotations, and editing notes that tell the cell how to read the book.

CNEwrap gives researchers a new way to search that hidden material.

And perhaps somewhere inside those billions of DNA letters is an evolutionary story we haven't read yet.

The exciting part is that we now have better tools to find it.

Read more about it https://academic.oup.com/nar/article/54/14/gkag709/8738333?

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0644-7

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

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Address of the bookmark: http://rrwick.github.io/Bandage/

java -Xms2G -Xmx4G -jar GenomeFinisher.jar  \
    -i target_contigs.fasta  \
    -ds alternative_assemblies.fasta -ref reference.fasta  \
    -o outputDirectory

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

An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnically-diverse human genomes.

https://f1000research.com/articles/7-1391/v1

Address of the bookmark: https://github.com/NCBI-Hackathons/NovoGraph