Illumina Sequencing Data Preprocessing

Illumina Universal adapters were removed and reads were trimmed using Trim Galore⁶³ with a minimum read length parameter 50 bp. The resulting reads were filtered using Kraken^{37 (link)}, as described below in Section 4.3, with a custom database built from the PhiX genome (NCBI Reference Sequence: NC_001422.1). Removal of PhiX content is suggested as it is a common contaminant in Illumina sequencing data^{64 (link)}. Trimmed non-PhiX reads were used in subsequent matrix filtering and microbial identification steps.

Free full text: Click here

Beck K.L., Haiminen N., Chambliss D., Edlund S., Kunitomi M., Huang B.C., Kong N., Ganesan B., Baker R., Markwell P., Kawas B., Davis M., Prill R.J., Krishnareddy H., Seabolt E., Marlowe C.H., Pierre S., Quintanar A., Parida L., Dubois G., Kaufman J, & Weimer B.C. (2021). Monitoring the microbiome for food safety and quality using deep shotgun sequencing. NPJ Science of Food, 5, 3.

Publication 2021

Universal adapters

Genome

Corresponding Organization :

Other organizations : IBM Research - Almaden

Top 5 similar protocols

Variable analysis

independent variables

Illumina Universal adapters removal
Reads trimming using Trim Galore with a minimum read length parameter 50 bp
Reads filtering using Kraken with a custom database built from the PhiX genome (NCBI Reference Sequence: NC_001422.1)

dependent variables

Trimmed non-PhiX reads

control variables

PhiX genome (NCBI Reference Sequence: NC_001422.1) as a control for Illumina sequencing data contamination

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!