Table 2 Assembly pipelines and descriptive statistics of PDB70 amplicon reads obtained with Illumina and MinION nanopore

From: A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra)

Pipeline

Type

Input

Error corrector

Contig assembler

Consensus size (bp)

GC%

Coveragea

Identity between chamois and Ovis aries DRB (GenBank AM884914)

CANU

De novo

MinION

Pilon

CANU

9001

40.86

×7139.92

95.81%

Geneious

De novo

MinION

Pilon

Geneious algorithm

9048

40.86

×7120.34

95.81%

DBG2OLC

Hybrid

Illumina, MinION

Pilon

Velvet (short reads)

8931

40.87

×7065.76

91.75%

  1. aThe coverage was calculated using Samtools (Li et al. 2009) considering Illumina reads mapped to Pilon-polished CANU, Geneious and DBG2OLC assemblies, respectively
Back to article page