UniqSketch: Sensitive and resource-efficient strain/abundance identification in metagenomics data

UniqSketch is a sensitive tool for identifying strains and their relative abundances in metagenomics samples. UniqSketch algorithm consists of two stages: Indexing and Querying.

• Indexing: the algorithm takes a list of target sequences (usually reference genomes) and then identifies all k-mers within each target in the list that uniquely belong to that specific sequence. It then checks a set of criteria such as low-complexity on the k-mer candidates to refine the list and provide the final set of unique k-mers for each target.
  To efficiently (memory and runtime) keep track of k-mers and their frequencies at indexing and querying stages, UniqSketch utilizes the Bloom filter data structure as an alternative for hash tables due to their costly computational resource requirements.
• Query: raw read sequencing data are queried against the sketch index. To remove the k-mers caused by sequencing errors (k-mers with very low depth), UniqSketch utilizes a cascading Bloom filter to discard weak k-mers and. The solid k-mers then queried against the index and the count for related reference target will be updated accordingly. After all solid k-mers in the raw read input data are queried, the reference count table is calculated computed to generate the final output of most abundant references.

Installation

UniqSketch builds into a stand-alone executable:

git clone https://github.com/amazon-science/uniqsketch
cd uniqsketch
make

Quick Start

UniqSketch consists of two modules:

• uniqsketch: for building a signature index from reference/target database
• querysketch: for querying the input read files against constructed index

1. Construct sketch index of size 81bp from three references, ref_1.fa, ref_2.fa, and ref_3.fa and store it in sketch_index:

uniqsketch --sensitive -k81 -o sketch_index.tsv ref_1.fa ref_2.fa ref_3.fa

2. Query a metagenomics sample with read files r1.fq.gz and r2.fq.gz:

querysketch --r1 r1.fq.gz --r2 r2.fq.gz --ref sketch_index.tsv --out out_sample.tsv 

Output

uniqsketch

• sketch_uniq.tsv: primary output file is a tab-separated file storing the final set of signatures for each reference in the universe.
• outdir_uniqsketch: folder contains a file per reference storing all signature candidates.
• db_uniq_count.tsv: a tab-separated file summarizing all references and total number of candidate signatures.

querysketch

• out_sample.tsv: primary output file reporting references and their abundance within the sample. The count column is the total number of uniqsketch signatures called by querysketch:

ref	abundance	count
-----------------------------
ref_1	0.7862		3033
ref_2	0.1993		769
ref_3	0.01426		55

• log_out_sample.tsv: detailed log showing for each reference the total number of assigned reads, and all signature:count.

Usage

uniqsketch

Usage: uniqsketch [OPTION] @LIST_FILES (or FILES)
Creates unique sketch from a list of fasta reference files.
A list of files containing file names in each row can be passed with @ prefix.

 Options:

  -t, --threads=N	use N parallel threads [1]
  -k, --kmer=N		the length of kmer [81]
  -b, --bit=N		use N bits per element in Bloom filter [128]
  -d, --hash1=N		distinct Bloom filter hash number [5]
  -s, --hash2=N		repeat BF hash number [5]
  -c, --cov=N		number of unique k-mers to represent a reference [100]
  -f, --outdir=STRING	dir for universe unique k-mers [outdir_uniqsketch]
  -o, --out=STRING	the output sketch file name [sketch_uniq.tsv]
  -r, --stat=STRING	the output unique kmer stat file name [db_uniq_count.tsv]
  -e, --entropy		sets the aggregate entropy rate threshold [0.65]
      --sensitive	sets sensitivity parameter c to 100
      --very-sensitive	sets sensitivity parameter c to 1000
      --help		display this help and exit
      --version		output version information and exit

querysketch

Usage: querysketch [OPTIONS] [ARGS]
Identify references and their abundance in FILE(S).

Acceptable file formats: fastq in compressed formats gz, bz, zip, xz.

 Options:

  -t, --threads=N	use N parallel threads [1]
  -b, --bit=N		use N bits per element in Bloom filter [64]
  -o, --out=STRING	the output file name
  -l, --r1=STRING	input read 1
  -r, --r2=STRING	input read 2
  -g, --ref=STRING	input uniqsketch reference
  -h, --hit=N		number of uniqsketch hits to call a refernce [10]
  -a, --acutoff=N	abundance cutoff to report [0.0]
  -s, --rcutoff=N	read cutoff to report [2]
      --sensitive	sets sensitivity parameter h=10
      --very-sensitive	sets sensitivity parameter h=5
      --solid		only use solid k-mers in reads
      --help		display this help and exit
      --versions	version information and exit