filterBALDR

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