This is a simple script for removing background noise from BALDR output before downstream processing.
System Requirements:
- Perl 5 with Pod::Usage and Statistics::Basic modules (tested on Perl 5.24.0, Pod::Usage 1.68, Statistics::Basic 1.6611)
Installation: < none >
Instructions for use:
- Generate CSV sample sheet with one line per cell:
- column 3 is the flow cell ID
- column 4 is the lane
- column 5 is the index/sequenceing barcode
- column 8 is the human readable cell ID (formatted as plate-well eg 1-A02 or 3-G8)
- Run BALDR, with output saved to a path that includes
<flowcell>/<lane> - Run BALDR summary scripts
perl filterBALDR.pl samplesheet.csv
For further usage details:
perl filterBALDR.pl -h
Expected output:
- Fasta file (
filtered.fa) of high quality contigs
Run time:
- Typically <1 second