Pipeline publication

[…] stom linker was ligated between the read-ends to facilitate mate-pair recovery. All libraries were sequenced for 100 cycles on a HiSeq2000 using the TruSeq SBS Sequencing Kit v.3. Data were analyzed with pipeline versions 1.8 and 1.9. An additional 5 kb mate-pair library was constructed and sequenced by the Beijing Genome Institute using pooled wasp genomic DNA with all reads trimmed to 36 bp before assembly., The custom 5 kb and 10 kb mate-pair libraries were filtered for reads containing properly-oriented reads of the appropriate insert size and uniqueness using in-house custom pipeline scripts. Raw Illumina reads were 5′- and 3′-trimmed for nucleotide-bias and low-quality bases using the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_tookit/). Trimmed reads were error-corrected by library with Quake counting 19-mers. SOAPdenovo v2.04 was employed with K = 49 to assemble the 180 bp-insert library reads followed by scaffolding with iteratively longer-insert mate-pair libraries and use of GapCloser v1.12 to close gaps generated in the scaffolding process with short paired read data ., MdBV DNA was isolated from virions as described previously . The DNA pellet was resuspended in 10 µl of H2O and 1 ul was used as template in four phi29 amplification reactions as performed previously . To resolve amplified DNA, the amplified product was incubated with S1 nuclease (NEB) at 37°C for 20 min. Precipitation and re-suspension in H2O yielded a total of 5 µg for Illumina sequencing. The sequencing library was prepared by the University of Georgia Genomics Facility using the Illumina TruSeq DNA sample preparation kit and the standard low-throughput protocol, and sequenced with the Illumi […]

Pipeline specifications

Software tools FASTX-Toolkit, Quake, SOAPdenovo
Organisms Human poliovirus 1 Mahoney, Viruses, Microplitis demolitor, Microplitis demolitor bracovirus