Plugins

Perform de novo multiple sequence alignment using MAFFT.

Add new sequences to an existing alignment with MAFFT.

Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).

Trim an existing alignment based on provided primers or specific, pre-defined positions. Primers take precedence over the positions,i.e. if both are provided, positions will be ignored.When using primers in combination with a DNA alignment, a new alignment will be generated to locate primer positions. Subsequently, start (5'-most) and end (3'-most) position from fwd and rev primer located within the new alignment is identified and used for slicing the original alignment. The retention of alignment positions that span the primer locations can be toggled. WARNING: finding alignment positions via primer search can be inefficient for very large alignments and is only recommended for small alignments. For large alignments providing specific alignment positions is ideal.

Record which sample, prepared DNA library, and sequencing run each read came from. This information is stored as BAM read groups and is used to combine runs from the same sample and interpret duplicates correctly. Supply the metadata table linking BAM filenames to sample and read-group identifiers. Preserve mode verifies existing labels and adds one group to an unlabeled BAM. Replace mode deliberately assigns one group to every read in a BAM. Reads from multiple unlabeled groups cannot be assigned to their original groups automatically.

Create a BAI lookup file beside each coordinate-sorted BAM so a caller or viewer can retrieve reads from a genomic region. The BAM contents are copied unchanged, and samtools verifies their coordinate order while building the index. Use this when the BAMs are already sorted. Unsorted input fails rather than being sorted automatically. The combined sample-preparation action performs this indexing internally. BAI supports contigs up to 512 Mb; CSI indexes are not produced.

Use GATK/Picard to identify reads that may be repeated observations of the same original DNA fragment. Choose mark to retain reads with duplicate flags, remove to discard identified duplicates, or skip to copy reads unchanged. Skip also preserves any existing duplicate flags. The choice depends on library preparation. For mark/remove, first combine a sample's sequencing runs into a coordinate-sorted BAM with correct library labels. Duplicate detection runs independently on each BAM. Outputs include the processed BAMs and duplicate metrics. This wrapper does not provide UMI-aware duplicate detection.

Combine the aligned reads from several lanes or sequencing runs into one BAM per sample. For example, lane1.bam and lane2.bam labeled sampleA become sampleA.bam; a BAM labeled sampleB stays separate. Sample labels come from the BAM read groups. Keep each run's read-group and library labels. Inputs must already be sorted by genome position and use matching reference contigs, lengths, and order. A sample with one BAM is copied under its sample name. This step creates no BAM indexes.