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ecc_finder Version: v1.0.0
ecc_finder identifies eccDNA loci using short and long reads.
To identify eccDNA loci by mapping to a reference genome.
Usage in details, please see the map-ont
usage: ecc_finder.py map-ont <reference.idx> <query.fq> (option)
usage: ecc_finder.py map-sr <reference.idx> <query.fq> (option)
usage: ecc_finder.py asm-ont <query.fq> (option)
usage: ecc_finder.py asm-sr <query.fq> (option)
All output is in eccFinder_output, or whichever directory -o specifies.
eccDNA.fasta
The eccDNA locus in FASTA format.
eccDNA.csv
The eccDNA locus in csv format.
| Col | Type | Description |
|---|---|---|
| 1 | string | Reference sequence name |
| 2 | int | Reference start on original strand |
| 3 | int | Reference start on original strand |
| 4 | int | Circular read number at the locus |
| 5 | int | Repeat units of all circular reads |
| 6 | int | Read coverage at the locus |
| 7 | int | EccDNA sequence length |