filter.merged.alignments.sh

Description

Filter alignments of physically overlapping target regions based on a minimum alingment score, which indicates whether the merging procedure was successful.

Usage

filter.merged.alignments.sh -d <directory> -s <numeric fraction>

Dependencies

Arguments

# Required
-d          Path to directory with merged alignments.

# Optional
-s  [0.95]  Minimum alignment score [between 0 and 1]. Overlapping alignments will only be retained if the
            merging procedure in `align.overlapping.contigs.sh` was successful, as indicated by the 
            visualizations and/or the alignment score.

Details

Alignment filtering is performed by moving unsuccessfully merged alignments to a separate subdirectory.

Value

Create a subdirectory in the directory passed via -d, where unsuccessfully merged alignments are placed.

Examples

filter.merged.alignments.sh -d mafft.overlapping.15 -s 0.95