MIGEC: Molecular Identifier Guided Error Correction pipeline

FEATURES

• De-multiplexing, adapter trimming and read overlapping for NGS data. Extraction of UMI sequences
• Assembly of consensuses for original molecules that entered library preparation by grouping reads with identical molecular identifiers
• Mapping of V, D and J segments, extraction of CDR3 regions and clonotype assembly for all human and mouse immune receptors (TRA/TRB/TRG/TRD and IGH/IGL/IGK)
• Additional filtering of hot-spot errors in CDR3 sequence
• Flexible and straightforward batch processing
• Currently all species-gene pairs that have germline sequences (based on IMGT) that allow CDR3 identification are supported

Species	Gene
HomoSapiens	TRA, TRB, TRG, TRD, IGL, IGK, IGH
MusMusculus	TRB, TRG, TRD, IGL, IGK, IGH
MacacaMulatta	TRB, IGK, IGH
OryctolagusCuniculus	IGL, IGK, IGH
RattusNorvegicus	IGL, IGH
CanisLupusFamiliaris	TRB, TRG
SusScrofa	IGL, IGK
BosTaurus	TRD
MusSpretus	IGL
GallusGallus	TRB
AnasPlatyrhynchos	TRB

Table of contents:

• Installing and running
• The pipeline
• De-multiplexing
• MIG statistics
• Consensus assembly
• V(D)J junction mapping
• Result filtering
• MIGEC log structure
• MIGEC analysis report
• Post-processing