ck7/compare-sets

The program compares two sets of DNA sequences (provided as FASTA files) and returns the percent of sequences in each set that align to sequences in the other set. It also provides alignment information for each sequence.

compare-sets

The program compares two sets of DNA sequences (provided as FASTA files) and returns the percent of sequences in each set that align to sequences in the other set. It also provides alignment information for each sequence. I wrote this program a while ago and later discovered this paper which was published in 2015 and takes a similar approach to genome comparison: https://academic.oup.com/nar/article/43/14/6761/2903001

Requirements

The program requires perl, bioperl and MUMmer (http://mummer.sourceforge.net/)

Usage

compare-sets.pl -1 <set1-scafs> -2 <set2-scafs> -o <out-prefix> [--silent] [-p <% identity threshold>]

Where

• set1-scafs is a DNA fasta file (genome, metagenome etc)
• set2-scafs is a second DNA fasta file
• out-prefix is the prefix for all output files (see below)
• --silent: No output at all except for error messages
• % identity threshold is the % identity that will be used to determine similarity (0..100, default: 96)

Output

compare-sets.pl will generate these files:

• <out-prefix>.coors, .delta - output for the Mummer programs
• <out-prefix>.report.txt - alignment report for each sequence. File looks as follows:

### GCF_001546235.1_ASM154623v1_genomic.fna ###

NZ_KQ955959.1	152422	90615	59.4
NZ_KQ955951.1	99091	86459	87.2
NZ_KQ955947.1	4015	0	0
NZ_KQ955953.1	2668	0	0
NZ_KQ955960.1	2545	2544	100
:
NZ_KQ955949.1	4452	0	0

1949214/2358436 (82.6%) are covered in GCF_001546235.1_ASM154623v1_genomic.fna

### GCF_002076055.1_Bbif1891B_genomic.fna ###

NZ_NAQG01000030.1	5942	0	0
NZ_NAQG01000014.1	8932	0	0
NZ_NAQG01000012.1	327702	285050	86.9
NZ_NAQG01000029.1	2039	595	29.1
NZ_NAQG01000003.1	8677	8005	92.2
:
NZ_NAQG01000015.1	22174	489	2.2

1977267/2418976 (81.7%) are covered in GCF_002076055.1_Bbif1891B_genomic.fna

Fields for each sequence are

<sequence-name> <sequence-length> <Number of bps covered by sequences from the other set> <% of bps covered by sequences from the other file>

Example

Download the example files, change directory to the example directory and use the following command line to generate the example output files:

compare-sets.pl -1 GCF_001546235.1_ASM154623v1_genomic.fna -2 GCF_002076055.1_Bbif1891B_genomic.fna -o comparison -p 90

compare-sets's Issues

Total percentage of similarity

Good program! Please tell me how you can calculate the total percentage of similarity between the two sets? And as I understand it, you can import the results of targeted sequencing into the program (for example 16S, g23)?