Transcriptomic Assembly Comparison: CLC Genomics vs Oyster River

Raw paired-end reads were quality-checked using FastQC (v0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) before transcriptomic assembly. Two assemblies were then made, first via the de novo assembly option in CLC Genomics WorkBench v.6.0.4 (CLCBio, Boston, MA) using raw reads, with scaffolding enabled, a minimum contig length of 200 bp, and automatic word and bubble sizes of 24 and 50, respectively. The second was assembled using the Oyster River Protocol (ORP, v2.2.6; [42 (link)]) and default settings (TPM_FILT = 1, STRAND = RF, MEM = 150, CPU = 24), on an Amazon Web Service EC2 server with 32 vCPUs and 128 GB of RAM. The first step in the ORP pipeline is read error correction via Rcorrector (v1.0.3), followed by Illumina adaptor removal and trimming of reads with Phred quality below 3, using Trimmomatic (v0.38). Trinity (v2.8.4; [43 (link)]), Spades55, Spades75 (v3.13.0; [44 (link)]) and Transabyss (v2.0.1; [45 (link)]) are then used to make four de novo assemblies, which are merged via a modified version of Orthofinder (v2.2.6; [46 (link)]) packaged in OrthoFuser [45 (link)]. The CLC and ORP-merged assemblies were assessed via BUSCO (v4.0.6; [47 ]) with the insecta_odb10 database, and TransRate (v1.0.3; [48 (link)]) read mapping.

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Gonzalez C.J., Hildebrandt T.R, & O’Donnell B. (2022). Characterizing Hox genes in mayflies (Ephemeroptera), with Hexagenia limbata as a new mayfly model. EvoDevo, 13, 15.

Publication 2022

CLC Genomics WorkBench v.6.0.4

Insecta Oyster River Transcriptomic

Corresponding Organization :

Other organizations : Plymouth State University

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Variable analysis

independent variables

Assembly method (CLC Genomics WorkBench vs. Oyster River Protocol)

dependent variables

Transcriptomic assembly quality (assessed via BUSCO and TransRate)

control variables

Minimum contig length (200 bp)
Automatic word and bubble sizes (24 and 50, respectively) for CLC Genomics WorkBench assembly
Default settings for Oyster River Protocol assembly (TPM_FILT = 1, STRAND = RF, MEM = 150, CPU = 24)
Amazon Web Service EC2 server with 32 vCPUs and 128 GB of RAM for Oyster River Protocol assembly

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