ccontigs

Detect contigs of complete circular genomes

Under the hood

As circular viral genomes are completely sequenced and assembled, the end of the genome is immediately followed by a repeat of the beginning of the genome. By recognizing the repeated start region of the genome, we can identify circular genomes that were completed and began repeating. This program ccontigs closes the circular genomic contigs by indeitfying repeats.

Performance

This program runs very rapidly thanks to the efficient pairwise alignment algorithms implemented in Julia.

The program ccontigs is able to identify all circular contigs with minimal false positive hits (i.e. linear contigs identified as circular). It is worth noting that some linear genomes were identified as circular. This is largely an artifact of naturally occuring repeats in some phage/virus genomes. As an example, the Staphylococcus phage MSA6 contains a repeat of the beginning of the genome at the end of the genome, even though it is linear (information from the source below). This rare occurence is important to note when interpreting results, as as minority of circular contigs may in fact represent artifacts. Because the goal is often detecting complete genome coverage instead of circular genomes themselves, these circular artifacts fail to diminish confidence of completely covered genomes.

On Mar 12, 2014 this sequence version replaced gi:394777096.
This sequence represents the complete sequence of MSA6 virion DNA.
MSA6 virion DNA contains 8049 bp direct sequence repeats at its
ends: L-LTR and R-LTR. Sequences of L-LTR and R-LTR are identical,
as one of them is generated during phage DNA packaging. Thus,
140194 bp of this sequence (L-LTR + non reduntant virion DNA part)
contain the complete set of MSA6 genes.

How to download

Simply download the set of files by clicking the releases button above and downloading the compressed file. You are also of course free to clone or fork the repository.

How to test the scripts

It is always important to test scripts before you run them. To this end, I encourage you to test the processes after downloading them. Do do this, simply open the terminal and move into the ccontigs directory. Then run the following:

bash testcode.sh

This will download and format a test dataset in the test directory using a set of pre-defined virus reference genomes, their accession numbers, and whether they have circular/linear genomes. Sequencing overlap was simulated by repeating the beginning of the genome at the end of the sequence. This overlap is used to detect a completed circular genome.

The output in your terminal should look something like this. If you fail any of the steps, you will need to fix the problem until they pass.

Running test
Downloading Sequences
--2016-09-11 18:57:45--  http://www.ebi.ac.uk/ena/data/view/KF482069,M14428,EF568108,X58839,CU468217,KC821618,KP063541,AB981169,JQ809663,KJ019160,K02718,FJ882854,KJ938717,KP133078,Z24758,GU071086,JQ234922,KF430219,GQ368252,JX051319,KP280063,GU071094,AY954962,EF177456,DQ163914,GU071103,AY500152,KF017927,KM279937,JN699002,FJ848881,KC690136,AJ556162,JF767208,AY526908,KF669652,JX080304,KM067278,KR902979&display=fasta
Resolving www.ebi.ac.uk... 193.62.193.80
Connecting to www.ebi.ac.uk|193.62.193.80|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: './tmpout'

./tmpout                                         [                            <=>                                                              ]   2.59M   436KB/s    in 6.1s    

2016-09-11 18:57:51 (434 KB/s) - './tmpout' saved [2717238]

Completed
Complete!
>>> PASS: Downloaded and formatted referece fasta
Perfect alignment score is 500
Complete
>>> PASS: ccontigs ran properly on reference file

How to run ccontigs

Once you have passed the tests, you are ready to run ccontigs. Simply run the script like this:

julia ccontigs.jl -i ./test/testout.fa -o ./test/juliaout.tsv

You may read more in the help menu by running the script as:

julia ccontigs.jl -h

Output will be as follows.

usage: ccontigs.jl [-i INPUT] [-o OUTPUT] [-l LENGTH] [-t THRESH] [-h]

optional arguments:
  -i, --input INPUT    Input fasta file for identifying circular
                       contigs.
  -o, --output OUTPUT  Output file to write reults.
  -l, --length LENGTH  Length of sequence window for detecting
                       repeats. (default: 100)
  -t, --thresh THRESH  Threshold (percent of length) for circular
                       contig. (default: 0.97)
  -h, --help           show this help message and exit