2.6 | Genome assembly
Following the pipeline of (Grau et al., 2018), de novo assembly of the target species genomes with in silico paired-ends and mate-pair reads were performed using SOAPdenovo2 (Luo et al., 2012). Firstly, the sparse pre-graph module was applied to use paired-end or simulated ancient DNA reads during de Brujin graph construction with the parameters, -g 15 -d 4 -e 4 -R -r 0, and parameter -M 1, during the contig phase. Secondly, in silico mate-pair reads generated by the original or optimized in silico method were mapped to contigs. Third, unique contigs were joined to scaffolds using mapped paired-end and mate-pair read information. For comparison with our optimized in silico mate-pair methods, we also used the RaGOO pipeline to perform genome assembly using the simulated ancient DNA reads with the following parameters: -f 1000 -d 100000 -i 0.2 -a 0.5 -s 0.5 -r -g 100 -m 10000. Unlike scaffolding by SOAPdenovo, the contigs produced by SOAPdenovo were ordered and oriented using RaGOO.