Up to 15% of contigs were discarded during filtering for prey contamination and even more are bacterial contaminants that could not be filtered out due to the lack of reference genomes.
After filtering for vector contamination and trimming for quality, the BESs were deposited in GenBank's GSS sequence repository: library AF_Bb has accessions ER936645- ER942217 and library AF_Bc has accessions ER967023- ER973759.
The reads obtained after QC are further filtered for primer contamination to improve and ensure quality of reads.
Furthermore, the reads were filtered for Wolbachia contamination by mapping (Bowtie2 (v2.1.0); Langmead and Salzberg 2012) to all Wolbachia strains available in GenBank.
This conservative approach was selected in order to filter for possible contamination with human DNA and remove spurious hits that could result from short sequencing reads.
After cloned sequences were filtered for vector contamination and quality, we obtained 2144 expressed sequence tags (ESTs; GenBank accession numbers: EG325041– EG325041).
Prior to assembly, all reads (in FASTQ format) were filtered for adapter contamination, ambiguous residues (N's) and low quality regions using nesoni v0.123 (http://www.vicbioinformatics.com/software.nesoni.shtml) with default settings.
Trimmed libraries were then filtered for rRNA contamination by mapping to a set of known rRNA sequences using Bowtie (Langmead et al. 2009) and allowing two mismatches in the 25 bp seed.
Each fastq file was QC filtered for artifact/process contamination and subsequently assembled with AllPathsLG release version R42328 with HAPLOIDIFY = True (Gnerre et al. 2011), resulting in the assembly detailed in table 2. We sequenced a single lane of Illumina reads for each of the additional species as well as an independent replicate of the A. muscaria genome.
After filtering for artifacts/ process contamination, the sequence data were assembled with Velvet 1.2.03 [ 146].
