Genome biologyBioinformaticsPeer-reviewed journal article
MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge
Kristen J. WadeiD, Rayo SusenoiD, Kerry Kizer, Jacqueline P. WilliamsiD, Juliano André BoquettiD, Stacy J. CaillieriD, Nicholas R. PollockiD, Adam RenscheniD, Adam SantanielloiD, Jorge R. OksenbergiD, Paul J. NormaniD, Danillo G. AugustoiD, Jill A. HollenbachiD
Abstract
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.
- organism: human
- assay: whole-genome sequencing
- research focus: genome assembly
- approach: experimental assay
- Citations
- 2
- FWCI
- 0.27
- Field percentile
- 48th percentile
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Complete sequences of six Major Histocompatibility Complex haplotypes, including all the major MHC class II structures
Torsten Houwaart, Stephan Scholz, … Alexander Dilthey·HLAPeer-reviewed·Mar 18, 2023
- A pan-MHC reference graph with 246 fully contiguous phased sequences
Liza Huijse, Solomon M. Adams, … Solomon Endlich·bioRxiv·Sep 1, 2023
- MAtCHap: an ultra fast algorithm for solving the single individual haplotype assembly problem.
Alberto Magi·bioRxiv·Dec 2, 2019
- A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex
Chen-Shan Chin, Justin Wagner, … Justin M. Zook·Nature CommunicationsPeer-reviewed·Sep 22, 2020
- Improved genome inference in the MHC using a population reference graph
Alexander Dilthey, Charles J Cox, … Gil McVean·bioRxiv·Jul 8, 2014
- HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads
Stefano Beretta, Murray Patterson, … Paola Bonizzoni·BMC BioinformaticsPeer-reviewed·Jul 3, 2018