Similar protocols

Pipeline publication

[…] as described [], using modified primers (Table ) and an optimised annealing temperature (58 °C), employing a suitable positive (A. cantonensis DNA recovered from Australian Rattus rattus) and negative (i.e. no template) controls. Individual PCR products were resolved in separate lanes on an agarose gel (1 % w/v) in TBE buffer (Tris/Borate/EDTA) and stained with SYBR®Safe gel stain (Life Technologies). Individual PCR products (~8 kb and 10 kb) were excised from the gel and purified using the QIAquick gel extraction kit (QIAGEN).Table 1, Short-insert libraries (100 bp) were constructed from the purified products and then sequenced using Mi-seq technology (Illumina platform; Yourgene, Taiwan). FastQC (Babraham Bioinformatics: www.bioinfomatics.babraham.ac.uk) was utilised to assess the quality of sequence data and the paired-end reads were filtered using Trimmomatic (http://www.usadellab.org/cms). De novo assembly of the sequences was performed using SPAdes 3.0.0 Genome Assembler (http://bioinf.spbau.ru/en/spades). The program was run for all odd k-mer sizes between 21 and 125 (inclusive). The k-mer size providing the largest scaffold was selected for further analysis., Following assembly, the mt genome of A. mackerrasae was annotated using a semi-automated bioinformatic pipeline []. Each protein coding mt gene was identified by local alignment comparison (performed in all six frames) using amino acid sequences from corresponding genes from mt genomes of A. vasorum, A. cantonensis and A. costaricensis; accession nos.NC_018602, GQ398121 and GQ398122, respectively [, ]. The large and small subunits (rrnL and rrnS) of mt ribosomal RNA genes were identified by local alignment, and all transfer RNA […]

Pipeline specifications

Software tools FastQC, Trimmomatic, SPAdes