To prepare sequencing library for SR sequencing, DNA was randomly sheared by sonication and 300–500 bp fraction was isolated by gel excision and used for Illumina paired-end (PE) following the instructions provided by the manufacturers. SR libraries used in this work include (1) 2 × 90 bp PE SR library, sequenced by HiSeq 2000 (BGI); (2) 2 × 150 bp PE SR library, sequenced by HiSeq X Ten (Macrogen Inc.); and (3) 2 × 150 bp mate-pair (MP) library with insert size of ~ 3 kb was also prepared and sequenced (BGI).
SR raw reads were processed by the following procedure. Raw reads were examined with FastQC33 (link) for base quality and the presence of adapters. AdapterRemoval tool34 (link),35 (link) was then used to remove the adapter sequences if present. Terminal ambiguous bases were trimmed off by Ambiguity trimming module of NGS QC Toolkit, and low quality reads were filtered out using IlluQC module of NGS QC Toolkit36 (link). Reads > = 100 bp were selected by PRINSEQ software37 (link). Mapping to reference genome was performed by BWA38 (link). The insert size of MP reads was estimated by BamTools-based script and reads with insert sizes of about 2600 (bp) +/− 30% were selected and used in assembly.
SR raw reads were processed by the following procedure. Raw reads were examined with FastQC33 (link) for base quality and the presence of adapters. AdapterRemoval tool34 (link),35 (link) was then used to remove the adapter sequences if present. Terminal ambiguous bases were trimmed off by Ambiguity trimming module of NGS QC Toolkit, and low quality reads were filtered out using IlluQC module of NGS QC Toolkit36 (link). Reads > = 100 bp were selected by PRINSEQ software37 (link). Mapping to reference genome was performed by BWA38 (link). The insert size of MP reads was estimated by BamTools-based script and reads with insert sizes of about 2600 (bp) +/− 30% were selected and used in assembly.
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