BBMerge

[…] m PHRED quality score of Q10 from the 3′ end using the BBDuk tool (http://jgi.doe.gov/data-and-tools/bbtools/). Trimmed reads shorter than 64 bases were discarded and the remainders were merged using BBMerge (http://jgi.doe.gov/data-and-tools/bbtools/). Both paired and unpaired reads were kept for de novo assembly, which was performed using SPAdes genome assembler 3.10.1 algorithm (Bankevich et al […]

[…] nc.) using the version 3 sequencing kit. A total of 1,491,678 paired-end reads (300 bp) were generated.Adapter sequences and low-quality bases were trimmed (bbduk), and overlapping pairs were merged (bbmerge) using the BBtools software suite (http://jgi.doe.gov/data-and-tools/bbtools/). Preprocessed reads were assembled using SPAdes version 3.10.1 () and polished with Pilon version 1.22 (). The as […]

[…] sorting. Reads with a final length <100 bp after adaptor clipping were discarded. Sequences were oriented into the forward and reverse primer direction. Forward and reverse reads were combined using BBMerge 34.48. Datasets of combined reads were analyzed in the SILVAngs analysis pipeline. Using the SILVA Incremental Aligner [SINA version 1.2.10 for ARB SVN (revision 21008)] () all sequence reads […]

[…] d used those previously identified variants for variant quality score filtering. Briefly, we performed adapter and quality trimming with TRIMMOMATIC v0.32 [], merged overlapping paired-end reads with BBMerge v5.4 (https://sourceforge.net/projects/bbmap/), aligned merged and unpaired reads and paired reads separately to the C. p. bellii 3.0.3 genome [] using BWA-MEM v0.7.12 [], then less stringentl […]

[…] files from the paired-read Illumina miSeq dataset were merged, trimmed, and normalized using the bbtools package (http://jgi.doe.gov/data-and-tools/bbtools) and Seqtk (https://github.com/lh3/seqtk). Bbmerge.sh was used to merge reads, and to trim primer sequences by setting the forcetrimleft parameter 22. All other parameters are set to default values. These reads were then mapped to the referenc […]

[…] first demultiplexed using GBSX () and filtered to remove any reads that did not match the barcode sequence used for library construction. Following demultiplexing, paired-end reads were merged using bbmerge in bbtools package (). Merged reads were next aligned to the 12X grapevine reference genome. Alignment BAM files where then used to generate a read count matrix with marker sequence tags, and […]