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The paired-end sequences were trimmed based on quality score by bTrim (Kong, unpublished, http://graphics.med.yale.edu/trim/readme).edu/trim/readme
Prior to de novo assembly, all obtained 40-mer reads were trimmed based on the phred quality value obtained using the Euler-SR qualitytrimmer command [26].
The candidate miRNA list was further trimmed based on the criteria as described [ 17, 42].
Reads were trimmed based on Phred quality scores at the probability threshold of p = 0.05.
The Illumina reads were first trimmed based on their quality scores using Btrim [ 45].
Alignments were trimmed based on levels of missing data, allowing for internal gaps ≤20 bp.
This database contains single pass sequencing reads that are not trimmed based on quality or vector contamination.
The 367 nucleotide alignments were then manually curated and trimmed, based on MASCE annotations of frameshifting events.
Another 67 positions were excluded by applying the 'strict' option (trimming based on an automatically selected sequence similarity threshold [ 59]).
Sequences were filtered and trimmed based on quality metrics and adapter sequences were removed with TrimmomaticPE [ 68].
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