Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

Bdelloid rotifers are small animals well known for their ability to survive in harsh conditions. They can endure extreme dehydration by entering a state of dormancy and then revive when water becomes available again. Scientists have always been interested in the degree to which these animals resist radiation, since radiation can severely damage DNA by causing both of its strands to break. Interestingly, Adineta vaga's ability to survive radiation may be connected to the way in which it tolerates drying out, as dehydration can also damage DNA. The rotifer probably evolved strong DNA protection and repair mechanisms primarily as a response to its severe environment. Its resistance to radiation is merely a byproduct of adapting to the cycles of drying and rehydration.

In order to find out more about this ability, the researchers subjected A. vaga to proton radiation and then examined what effect it had on its chromosomes. The radiation caused serious damage, resulting in hundreds of breaks in the DNA. For the vast majority of organisms, such extensive chromosome damage would be disastrous; it's similar to going through an instruction manual in a shredder and ending up with a large number of separate fragments. The scientists believed that the rotifers would repair their chromosomes before producing offspring. However, what they discovered was unexpected: some of the broken pieces of chromosome did survive and were passed on to the next generations, where the repair process continued.

The discovery took on even greater interest when the scientists examined the offspring of the irradiated rotifers. Rather than observing the same DNA damage in all the generations, they found different sized sections missing and evidence that some of the genetic regions which had been lost were being slowly restored. The researchers proposed that the rotifers use a repair mechanism known as Break-Induced Homologous Extension Repair, or BIHER. In simple terms, a broken piece of DNA can locate a matching sequence on the other chromosome and use it as a guide to rebuild itself. If the damage is beyond what can be repaired in one generation, the repair process can continue in the next.

What makes the rotifer's method of repairing DNA so unusual is that, normally, we consider DNA repair to take place immediately after damage has occurred, with the cell rapidly repairing the damaged DNA. In A. vaga, however, the repair process can be a lot longer. Certain pieces of chromosome survive the initial damage, are inherited, and then serve as the basis for further repairs in later generations. It's as if one generation begins mending a broken book, the next one continues the work, and another eventually completes the job until all the missing parts have been restored.

One reason why this might work is that bdelloid rotifers have holocentric chromosomes. Rather than having a single point, as most chromosomes do, which controls movement during cell division, the ability to move is distributed along the entire length of their chromosomes. As a result, fragments of chromosomes are sometimes able to retain the parts that are necessary for them to move and divide, and this may account for how broken pieces of chromosome can last long enough to be passed on and then repaired.

This finding could have implications that go beyond those concerning rotifers. Scientists are interested in understanding how genomes cope with severe chromosome damage, for example in the case of chromothripsis, where chromosomes break and are then reassembled in new configurations. Investigating A. vaga could help us to learn how cells manage large genetic issues. Moreover, its high resistance to radiation might also prove useful in research into extreme environments, such as the radiation hazards encountered on long space missions. However, these are ideas for future investigation; at present the rotifer's DNA repair mechanism cannot be used to protect people from radiation.

What is perhaps the most interesting aspect of this discovery is that the rotifer's remarkable ability could have developed for a very simple reason. Since an animal living in moss constantly undergoes periods of drying out and then getting wet again, the same mechanisms that protect its DNA when it is dehydrated might also enable it to survive radiation which would damage most other animals. Therefore, the rotifer probably did not evolve solely in order to resist radiation; instead, it became extremely good at coping with the difficult conditions it encounters, and radiation resistance was just a byproduct.

The case of Adineta vaga demonstrates that survival does not always mean avoiding damage; on some occasions it involves being able to recover from damage which appears to be impossible to repair. This small animal can survive having its chromosomes broken into many pieces, retain some of those pieces, pass them on to its offspring, and continue to repair them over successive generations. Although we generally regard DNA as something fragile that must always remain intact, the rotifer indicates an alternative possibility: perhaps a genome does not have to be perfect in order to survive, since sometimes the pieces last long enough for life to reassemble them, bit by bit, generation after generation.

Ream more at https://www.science.org/doi/10.1126/sciadv.aee0891

Usage: perl run_rcorrector.pl [OPTIONS]
OPTIONS:
	Required
	-s seq_files: comma separated files for single-end data sets
	-1 seq_files_left: comma separated files for the first mate in the paried-end data sets
	-2 seq_files_right: comma separated files for the second mate in the paired-end data sets
	-i seq_files_interleaved: comma sperated files for interleaved paired-end data sets
	Optional
	-k INT: kmer_length (<=32, default: 23)
	-od STRING: output_file_directory (default: ./)
	-t INT: number of threads to use (default: 1)
	-trim : allow trimming (default: false)
	-maxcorK INT: the maximum number of correction within k-bp window (default: 4)
	-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)
	-ek INT: expected number of kmers; does not affect the correctness of program but affects the memory usage (default: 100000000)
	-stdout: output the corrected reads to stdout (default: not used)
	-verbose: output some correction information to stdout (default: not used)
	-stage INT: start from which stage (default: 0)
		0-start from begining(storing kmers in bloom filter) ;
		1-start from count kmers showed up in bloom filter;
		2-start from dumping kmer counts into a jf_dump file;
		3-start from error correction.

Address of the bookmark: https://github.com/mourisl/Rcorrector/

Address of the bookmark: https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings

This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically.

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

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

(1) Convert genome position from one genome assembly to another genome assembly

In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

(2) Convert dbSNP rs number from one build to another

(3) Convert both genome position and dbSNP rs number over different versions

Run:

liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed

The outformat is as follow:

Deleted in new:
    Sequence intersects no chains
Partially deleted in new:
    Sequence insufficiently intersects one chain
Split in new:
    Sequence insufficiently intersects multiple chains
Duplicated in new:
    Sequence sufficiently intersects multiple chains
Boundary problem:
    Missing start or end base in an exon

For example:

If you liftOver chr4:6497-6497 from hg19 to GRch38 and it return "deleted in new". 

It means chr4:6497-6497 is part of a genomic contig on hg19 that is not anymore mapped on GRch38 because the new assembly is now better built without including this contig.

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

Address of the bookmark: https://bernatgel.github.io/karyoploter_tutorial/