Skills with input "Read-group metadata"

bio-read-alignment-bwa-alignment - Align DNA short reads with BWA-MEM2

DNA sequencing short-read alignment BWA-MEM2 reference genome

★ 6 · Updated 2026-10-04

Align paired-end or single-end DNA short reads to a reference genome with BWA-MEM2 or BWA-MEM, including read groups and BAM output preparation.

⚙ Align paired-end reads ⚙ Align single-end reads ⚙ Build reference indexes

bio-duplicate-handling - Mark or remove PCR and optical duplicates

bioinformatics BAM duplicate marking samtools

★ 0 · Updated 2026-10-01

Marks or removes PCR and optical duplicates in BAM alignments with samtools fixmate and markdup, with assay-specific guidance on when duplicate handling is inappropriate.

⚙ Mark PCR duplicates ⚙ Remove duplicate reads ⚙ Detect optical duplicates

bio-duplicate-handling - Mark or remove PCR and optical duplicates

bioinformatics BAM sequencing duplicate handling

★ 0 · Updated 2026-09-29

Marks or removes PCR and optical duplicates in BAM files with samtools fixmate and markdup for downstream analysis.

⚙ Sort BAM alignments ⚙ Add mate tags ⚙ Mark duplicate reads