Identifying amino acid sequences using sequenced reads
Lapidary uses Diamond to identify reads that align to an amino acid sequence database and calculates the amino acid coverage, identity and mean read depth using the translated sections of the read alignment.
Bring up the full list of options:
%perl Lapidary.pl -version
Lapidary: a software for identifying amino acid sequences using sequenced reads
Options:
read_1 Location of first read file (required)
read_2 Location of second read file if read files are paired
db Full location to fasta file containing amino acid sequences (required)
threads Number of threads to use for Diamond (default: 1)
identity Diamond identity percentage cut-off to use (default: 70)
coverage Diamond coverage percentage cut-off to use (default: 50)
read_type Types of reads used (required): single or paired
sequence_identification Method for calling most likely sequence: identity (default) or consensus
help Display help screen
version Return version of Lapidary
Run Lapidary on single read files:
perl Lapidary.pl -read_1 Examples/Reads/Single_reads.fq.gz --read_type single -db Examples/Amino_acid_database.fasta
Run Lapidary on paired read files:
perl Lapidary.pl -read_1 Examples/Reads/Paired_reads_1.fq.gz -read_2 Examples/Reads/Paired_reads_2.fq.gz -read_type paired -db Examples/Amino_acid_database.fasta
Lapidary produces a tab-delimited file for each read file or read pair with the following columns:
| Column | Description | Example |
|---|---|---|
| Protein | Reference amino acid sequence | BAC0273 |
| Coverage | Proportion of reference amino acid sequence that reads alined to | 0.7563248764 |
| Identity | Identity proportion between reads and reference amino acid sequence and reads | 0.9515154354 |
| Mean_read_depth | Mean read depth for the reference amino acid sequence | 1.2111562156 |
| Alignment_start | Position of first amino acid that reads aligned to | 23 |
| Alignment_end | Position of last amino acid that reads aligned to | 324 |
| Most_likely_sequence | Most likely sequence predicted | VGVAVYELDLFGRLRNL |
- perl >=5.32
- diamond >=2.1.7
Lapidary can be installed using the following cpanm command:
cpanm App::lapidary
A web interface is available to run Lapidary on paired read files: https://lapidary.quadram.ac.uk/