SARS-COV2_LCRs is a short pipeline to plot low complexity regions (LCRs) prevalence from SARS-CoV2 genbank files, using NCBI seg output. It's main objective is to automatize seg analysis and easily locate LCRs of interest in SARS-CoV2 proteomes.

This scripts were used for LCRs detection in the article "Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein".

Dependencies

These are SARS-COV2_LCRs dependencies, links to their installing instructions, commands for installation, and used versions:

It also assumes properly functioning perl (tested with v5.30.0), and seg working under any location. For instance, this is the expected output of entering seg at commnand line:

Usage: seg <file> <window> <locut> <hicut> <options>
         <file>   - filename containing fasta-formatted sequence(s) 
         <window> - OPTIONAL window size (default 12) 
         <locut>  - OPTIONAL low (trigger) complexity (default 2.2) 
         <hicut>  - OPTIONAL high (extension) complexity (default locut + 0.3) 
	 <options> 
            -x  each input sequence is represented by a single output 
                sequence with low-complexity regions replaced by 
                strings of 'x' characters 
            -c <chars> number of sequence characters/line (default 60)
            -m <size> minimum length for a high-complexity segment 
                (default 0).  Shorter segments are merged with adjacent 
                low-complexity segments 
            -l  show only low-complexity segments (fasta format) 
            -h  show only high-complexity segments (fasta format) 
            -a  show all segments (fasta format) 
            -n  do not add complexity information to the header line 
            -o  show overlapping low-complexity segments (default merge) 
            -t <maxtrim> maximum trimming of raw segment (default 100) 
            -p  prettyprint each segmented sequence (tree format) 
            -q  prettyprint each segmented sequence (block format)

Cloning this repo

To clone this repo via command line git, enter the following commands:

git clone https://github.com/abelardoacm/SARS-COV2_LCRs.git
cd SARS-COV2_LCRs/bin/
chmod +x *

if all requirements are met you should be ready to go

Repo tree

.
├── bin <-  Where you have to be to invoke scripts
│
├── data
│   └── Raw_database <- Place here genomic genbank files 
│
└── results

Using SARS-COV2_LCRs

This repository contains all the scripts used in the research article titled: "Two Short Low Complexity Regions (LCRs) are Hallmark Sequences of the Delta SARS-CoV- 2 Variant Spike Protein", currently published in Scientific Reports (Becerra et al., 2022). To access the complete database, please check the supplementary files for the list of NCBI accession IDs of analyzed files for each variant. A sample dataset containing Beta variant genomes is shared here.

To reproduce the analysis, from /bin/ type the following command:

./SARS-COV2_LCRs.sh

you will be prompted for the seg parameters one at a time (we used, window = 12, locut = 1.9 and hicut = 2.1).

Note that the previous command performs the full analysis for each .gb file contained in /data/Raw_database/. It begins invoking BD_seg.sh, which reads each .gb file to build a fasta file with genomic coordinates on headers. Then NCBI seg is used via Just_a_seg_envelope.sh. Output is saved in a csv file suitable for exploration with R. The pipeline continues with the script Analyze_LCRs.R that computes counts of the SARS-CoV2 LCRs of interest and exports .tiff barplots to results. Finally, Plot_proteome_complexity.R graphs the estimated average complexity for each position in analyzed proteomes per file.