IMPLICON UMI transfer

The option --implicon is a similar run-and-exit specialty mode for paired-end libraries where the UMI lives at the 5' end of Read 2 only. It transfers the first N bases of R2 into the read ID of both reads (as :BARCODE), then clips R2 by N bases. Read 1 is otherwise untouched. In Perl v0.6.x the UMI length was hardcoded at 8 bp; v2.x takes an optional value (--implicon=12, for example) with a default of 8.

Output filenames follow the pattern {stem}_{N}bp_UMI_R1.fastq(.gz) / {stem}_{N}bp_UMI_R2.fastq(.gz). Like --clock, Trim Galore exits after the transfer; the resulting files are then run through a second Trim Galore invocation for adapter and quality trimming.

Workflow

# Step 1: IMPLICON UMI transfer
trim_galore --implicon --paired sample_R1.fq.gz sample_R2.fq.gz

# Step 2: adapter / quality trim
trim_galore --paired sample_8bp_UMI_R1.fastq.gz sample_8bp_UMI_R2.fastq.gz

The downstream alignment and deduplication tooling parses the UMI back out of the read ID.

Multi-pair input

Since v2.1.0-beta.4, --implicon accepts any even number of inputs as consecutive R1/R2 pairs:

trim_galore --implicon A_R1.fq.gz A_R2.fq.gz B_R1.fq.gz B_R2.fq.gz

Each pair gets a header (=== IMPLICON pair N of M ===) and the same output-collision pre-flight (case-insensitive, full-path) that --paired runs. Pairwise (R1, R2, R1, R2, …) order is required; don't pass *R1.fq.gz *R2.fq.gz globs (those produce all-R1s-then-all-R2s).