Description of file formats used in D-Genies
PAF (Pairwise mApping Format)
Default output format of minimap2.
It's a tabulated file. Description of columns below.
|1||string||Query sequence name|
|2||int||Query sequence length|
|3||int||Query start coordinate (0-based)|
|4||int||Query end coordinate (0-based)|
|5||char||‘+’ if query/target on the same strand; ‘-’ if opposite|
|6||string||Target sequence name|
|7||int||Target sequence length|
|8||int||Target start on original strand (0-based)|
|9||int||Target end on original strand (0-based)|
|10||int||Number of matching bases in the mapping|
|11||int||Number bases, including gaps, in the mapping|
|12||int||Mapping quality (0-255; 255 for missing)|
Column 11 gives the total number of sequence matches, mismatches and gaps in the alignment; column 10 divided by column 11 gives the BLAST-like alignment identity.
PAF may optionally have additional fields in the SAM-like typed key-value format. Minimap2 may output the following tags:
|tp||A||Type of aln: P/primary, S/secondary and I,i/inversion|
|cm||i||Number of minimizers on the chain|
|s2||i||Chaining score of the best secondary chain|
|NM||i||Total number of mismatches and gaps in the alignment|
|AS||i||DP alignment score|
|ms||i||DP score of the max scoring segment in the alignment|
|nn||i||Number of ambiguous bases in the alignment|
Source: minimap2 documentation.
Maf (Multiple Alignment File)
Description of the format is available here.
Index files used in D-Genies are built as follow.
First line contains the name of the sample. Next lines describes contigs of the sample. They are composed of two columns, tab separated. First it the name of the contig, second it's size in bases.
Homo sapiens chr1 248956422 chr2 242193529 chr3 198295559
Backup file is a TAR archive. It contains three files:
- The alignment file, in paf format, named
- The target index, named
- The query index, named
Names of files must be kept. Otherwise, the backup file will not be accepted by the run form.