When -c is specified, a PAF output that contains signal to read alignment is generated. Please refer here for a detailed explanation of the specification, along with examples. Note that in Squigulator’s context the target sequence (column 6 to 9 in PAF) refers to the perfect sequences output through -q option (rather than basecalled reads in here). So when reading that specification, assume that the basecalled sequences refers to output generated through -q.
When –paf-ref is specified along with -c, the ouput PAF file will contain signal to reference alignment information (rather than signal to read). The target reference (column 6 to 9 in PAF) will contain the reference sequence information, rather than the read in this case.
When -a is specified, a SAM file that contains signal to reference alignment information is created.
| Col | Type | Name | Description |
|---|---|---|---|
| 1 | string | QNAME | Read identifier name |
| 2 | int | FLAG | Bitwise flag (0 if “+” strand and 16 if ‘-‘) |
| 3 | string | RNAME | Reference sequence name |
| 4 | int | POS | Reference sequence start index for the mapping (1-based; open) |
| 5 | int | mapq | Mapping quality (always 255) |
| 6 | string | CIGAR | CIGAR string (read to reference) |
| 7 | string | RNEXT | always “*” |
| 8 | int | PNEXT | always 0 |
| 9 | int | TLEN | always 0 |
| 10 | string | SEQ | the simulated perfect read sequence directly extracted from the reference |
| 11 | string | QUAL | always “*” |
Following optional tags are present:
| Tag | Type | Description |
|---|---|---|
| si | Z | coordinates associated with the ss tag below (explained below) |
| ss | Z | signal alignment string in format described here |
si tag contains four comma separated values start_raw, end_raw, start_kmer and end_kmer, respectively. Those values have the same as the columns 3,4,8 and 9 in the PAF format explained above when –paf-ref is specified along with -c