FastUniq

[…] in dataset i, including the first sample, which is technically a vegetative mycelium sample. the compost dataset exhibited high amounts of pcr duplicates (si appendix n), which we removed using fastuniq (32)., the p1 and p2 genomes (13) were annotated with braker1 (33) and augustus 3.0.2 (34) using the pooled rna-seq data from the mushroom tissue dataset (si appendix o). named genes […]

[…] preprocessed in three steps before using them for extending pacbio contigs: a) using trimmomatic [63], from both ends of reads, nucleotides with base quality lower than 15 were removed. b) using fastuniq [64], duplicate pairs were removed from the pe library, and c) soapec [65] was used to correct read error [64, 65]. any initial genome sequence has bacterial contamination due, at least, […]

[…] was fragmented, exome-enriched, and sequenced (illumina [san diego, ca] truseq 62 mb and hiseq 2000, 100 bp paired-end reads). bioinformatic analysis included duplicate sequence read removal with fastuniq,7 alignment to ucsc hg19 with bwa8 variant detection with freebayes, and variant annotation with annovar. variants were annotated as exonic/splicing, excluding synonymous variants, […]

[…] reads per sample. the reads were of high quality (>97% passed tailing:30 criteria using trimmomatic [bolger et al., 2014]) and included very few duplicates (approximately 2%, as assessed using fastuniq [xu et al., 2012]). trinity was used for de novo assembly of the reference transcriptome (see materials and methods), which was composed of 4.3 million contigs and isoforms (referred […]