FastUniq

[…] 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, […]

[…] 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 […]

[…] diego, ca, usa) following the 100 bp paired-end genomic dna sequencing protocol., the sequence reads from chip and input dnas (chip-seq and input-seq reads, respectively) were first treated using fastuniq56 and trimmomatic57 to remove pcr duplication and low quality reads. a two-step procedure7 was adopted with some modifications to determine the centromeric repetitive sequences. first, […]

[…] used raw reads for the above assemblies, but the reads underwent a quality-control screening before being back-mapped to contigs with the following procedure: (i) duplicated reads were removed using fastuniq (99); (ii) paired-end reads were merged with flash, and the merged and unmerged reads were kept; (iii) reads were removed if the percentage of high-quality nucleotide positions (i.e., […]

[…] 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, […]