Lima
Supported Tool
Lima, the PacBio barcode demultiplexer, is the standard tool to identify barcode sequences in PacBio single-molecule sequencing data. Starting in SMRT Link v5.1.0, it is the tool that powers the Demultiplex Barcodes GUI-based analysis application.
Description
The Lima module parses the report and count files generated by Lima, a PacBio tool to demultiplex PacBio single-molecule sequencing data.
By default, Lima will use barcode1--barcode2 as the sample names. To prevent
these barcodes showing up in the General Statistics table of MultiQC, the Lima
results are added to their own section.
If you want to include the Lima results in the General Statistics table, you
can rename the barcode1--barcode2 filenames to their apropriate samples using
the —replace-names
option. Each sample that is specified in this way will be moved from the Lima
section to the General Statistics table.
File search patterns
lima/summary:
contents: ZMWs above all thresholds
num_lines: 2
max_filesize: 1024
lima/counts:
contents: IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore
num_lines: 1
qualimap/bamqc/genome_results:
fn: genome_results.txt
qualimap/bamqc/coverage:
fn: coverage_histogram.txt
qualimap/bamqc/insert_size:
fn: insert_size_histogram.txt
qualimap/bamqc/genome_fraction:
fn: genome_fraction_coverage.txt
qualimap/bamqc/gc_dist:
fn: mapped_reads_gc-content_distribution.txt
qualimap/rnaseq/rnaseq_results:
fn: rnaseq_qc_results.txt
qualimap/rnaseq/coverage:
fn: coverage_profile_along_genes_(total).txt