To perform the de novo assembly, the reads produced by Illumina sequencing from all the four libraries were aligned against the filtered public data set using SOAP2 aligner [ 76].
All read libraries were aligned to a reference consisting of 1392 scaffolds derived from the Anopheles funestus FUMOZ colony with the An.
Quality- and adapter-trimmed reads for all 60 libraries were aligned to the transcriptome using the align_and_estimate_abundance.pl script in the Trinity r20140413 toolkit, which uses Bowtie (version 0.12.7) for alignment and RSEM (version 1.2.10) for estimating transcript abundance.
Raw reads from all whole transcriptome RNA-seq libraries were aligned using a two-step alignment approach.
For the identification of piRNA-like RNAs, all non-annotated sequences from B. germanica libraries were aligned against piRNA sequences found in the GenBank and D. melanogaster transposon database (FlyBase).
The libraries were aligned with the mango transcriptome at alignment rates (mapped reads/total reads) of 90.84, 90.02, 89.48, 89.77, 90.70, 90.11, 90.25 and 90.35% for samples 1 to 8, respectively.
All McrA sequences derived from the SHS method and metagenomic libraries were aligned to a sequence obtained from the amplicon library.
Millions of raw reads obtained from ChIP-Seq libraries were aligned to the reference soybean genome using the ultrafast Bowtie aligner [ 34] to obtain quantitative data for genome matched reads.
Both preprocessing steps were implemented as Perl scripts and led to a speed-up of all further computations by a factor of about 18. Processed libraries were aligned to miRBase release 14.0 with NCBI BLAST (blastall version 2.2.18) using standard settings without DUST filter (option -F F).
