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The rifH stop codon was then removed to enable translational read through to xylE (pAP47, not shown).

PRINSEQ (lite 0.14.4) [ 37] was used to remove redundant reads, to trim low quality reads (average QV < 20 for a 3-nt window, and QV < 18) and to remove small pre-processed reads (read length < 30 bp) [ 37].

In order to further characterize the A. syriaca nuclear genome, BLAT was used to remove reads corresponding to nuclear rDNA and the chloroplast and mitochondrial genomes using the sequences generated through reference guided assembly.

For most datasets, the sequence cleaning step usually includes filtering to remove read duplicates, low quality reads, contaminating sequences, and adaptor or barcode sequences.

Raw data was filtered by BGI to remove read pairs where either read contained adapters or greater than 50% of bases with a quality value <= 5.

Atlas genome assembly tools [97] were used to process reads, to remove repetitive reads, and to bin overlapping reads before assembling the contigs with the program PHRAP [95].

The default parameters for quality filtering in MG-RAST were used to remove reads with bad quality and to remove artificial sequence duplicates.

After filtering to remove reads that failed to match the haploid DNA, 1156 million reads (69%) remained.

Aligned reads were filtered using SAMtools (v0.1.9) to remove reads that failed to form a correctly aligned pair (forward and reverse templates).

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