kobie-kirven / scims

Sex Calling for Metagenomic Sequences

• What is SCiMS?
• Installation
• Usage
• Install Requirements
• Quick Tutorial

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What is SCiMS?

SCiMS (Sex Calling for Metagenomic Sequences) is a tool for determining host sex using shotgun metagenomic data. Currently, this tool supports sex determination for host organisms that contain two sex chromosomes. (Ex. X and Y in humans). Briefly, SCiMS works by aligning shotgun metagenomic data to a reference genome and comparing the coverage of the homogametic chromosome to the coverage of the autosomes.

Installation

Requirements

• bowtie2==2.4.4
• Samtools==1.13

All of the required tools can be installed with conda (see Install Requirements)

SCiMS can be easily installed with:

pip3 install git+https://github.com/Kobie-Kirven/SCiMS

Usage

• SCiMS is designed to work with both single and paired-end metagenomic data. The command-line usage is:

  usage: scims [-h] [-v] [--bowtie-index INDEX] [--ref-genome REF] [--scaffold-names SCAFFOLD] [-1 FORWARD] [-2 REVERSE] [-s SINGLE] [--x HOMOGAMETIC]
           [--y HETEROGAMETIC] --o OUTPUT [--t THREADS] [--from-sam FROM_SAM] [--get-scaffold-lengths LENGTHS] [--scaffold-lengths SCAF_LENGTHS]
  Sex Calling for Metagenomic Sequences
  options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --bowtie-index INDEX  Path to Bowtie2 index
  --ref-genome REF      Reference genome in FASTA or FASTA.gz format
  --scaffold-names SCAFFOLD
                         Path to file with scaffold names
  -1 FORWARD            Forward reads in FASTA or FASTQ format (PE mode only)
  -2 REVERSE            Reverse reads in FASTA or FASTQ format (PE mode only)
  -s SINGLE             Single-end reads in FASTA or FASTQ format (SE mode only)
  --x HOMOGAMETIC       ID of homogametic sex chromosome (ex. X)
  --y HETEROGAMETIC     ID of heterogametic sex chromesome (ex. Y)
  --o OUTPUT            Output plot prefix
  --t THREADS           Number of threads to use
  --from-sam FROM_SAM   Use sam file instead of preforming the alignment
  --get-scaffold-lengths LENGTHS
                         Determine scaffold lengths
  --scaffold-lengths SCAF_LENGTHS
                         Path to file with scaffold lengths
  

Install Requirements

To install the required tools with conda, run the following code.

conda install -c bioconda bowtie2
conda install -c bioconda samtools

Note: For some reason, the current version of Bowtie2 has an issue with tbb. To fix this, run

conda install tbb=2020.2

Quick Tutorial

This tutorial is intended to ensure that your SCiMS installation is working correctly:

Directly from SAM file

1. Download test files:

   wget https://github.com/Kobie-Kirven/SCiMS/raw/main/test_data/male_test.sam
   wget https://github.com/Kobie-Kirven/SCiMS/raw/main/test_data/scaffold_lengths.txt
   wget https://github.com/Kobie-Kirven/SCiMS/raw/main/test_data/scaffolds.txt

2. Run SCiMS in alignment-free mode:

   scims_test]$ scims --scaffold-names scaffolds.txt --x NC_000023.11 --y NC_000024.10 --o test --t 1 --from-sam male_test.sam --scaffold-lengths scaffold_lengths.txt
   

3. You should see output similar to the following:

   Using SAM file
   Extracting propper alignments:
         A total of 18449 alignments met the criteria
   The average NC_000024.10:NC_000023.11 ratio for the file was 0.5285776962795797
   

   

Preform alignment first

1. Download sequence files

wget https://github.com/Kobie-Kirven/SCiMS/raw/main/test_data/female_10000_1.fa
wget https://github.com/Kobie-Kirven/SCiMS/raw/main/test_data/female_10000_2.fa

2. Download reference genome

wget https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz

3. Build the Bowtie2 index

bowtie2-build GRCh38_latest_genomic.fna.gz GRCh38_latest_genomic.fna.gz

5. Run SCiMS in alignment-free mode:

   scims --scaffold-names scaffolds.txt --x NC_000023.11 --y NC_000024.10 --o test --t 1 -1 female_10000_1.fa -2 female_10000_2.fa --scaffold-lengths scaffold_lengths.txt --bowtie-index GRCh38_latest_genomic.fna.gz
   

6. You should see output similar to the following:

   Aligning sequences to GRCh38_latest_genomic.fna.gz:
   Forward reads: female_10000_1.fa
   Reverse reads: female_10000_2.fa
   Extracting propper alignments:
         A total of 18552 alignments met the criteria
   The average NC_000024.10:NC_000023.11 ratio for the file was 0.9519628016280371