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Mr. Levine led them in a vigorous, trim reading in which the often delicate instrumental strands were finely balanced.
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DynamicTrim from the SolexaQA package version 2.2 [ 42] was used to trim reads.
Therefore, it was not necessary to trim reads to remove the adapter sequences.
The Novoalign aligner, which has enhanced ability to trim reads to obtain a match, confidently mapped reads here merely because they contained a long polyA string.
A custom script was used to trim reads of 3' adapter sequences and then to pool identical reads to create a non-redundant sequences (=signatures) list.
The trimmed reads were then grouped into unique reads.
The trimmed reads were aligned to reference sequence by means of BWA with default parameters (v0.7.13).
Reference transcriptome was assembled with trimmed reads using Trinity (v2.0.6) (Grabherr et al. 2011; Haas et al. 2013).
Table S2: Raw and trimmed reads, Good's coverage, Chao1, ACE, Shannon, Simpson, and plus numbers of OTUs of the activated sludge samples.
The resulting trimmed reads were checked for contaminants, and low quality bases and contaminants were removed using the cutadapt software (Martin 2011).
We trimmed reads to a common length of 28 nt to avoid aligning sequenced amplification primers.
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