SMaHT Pipelines Documentation

Welcome to the documentation for SMaHT analysis pipelines and associated resources.

CONTENTS

PREPROCESSING

• FASTQ Files: Overview / polyG Artifacts Removal

ALIGNMENT

• Short-Read Illumina, Paired-End: Overview / Alignment / Read Groups / Duplicate Reads / Local Realignment / Base Quality Score Recalibration / Hi-C

• Long-Read PacBio HiFi: Overview / Alignment / Read Groups / Methylation and Tags

• Long-Read Oxford Nanopore: Overview / Alignment / Read Groups / Methylation and Tags

REFERENCE FILES

• Genome Builds: Overview / Build GRCh38

• Variant Catalogs: Overview / dbSNP / Mills_and_1kGP

CHANGELOG