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