Adapter_Trimming

Basic Usage

The Adapter_Trimming handler trims junk adapter sequences off of sample reads. This script utilizes Scythe, which can be run on paired-end or single-end data. Adapter_Trimming takes FastQ, FastA, or gzipped FastQ/FastA files as input and returns gzipped FastQ or FastA files. Scythe uses a Bayesian model with a prior contaminant estimate instead of a fixed number of mismatches. For more information, please read the Scythe documentation. To run Adapter_Trimming, all common and wrapper-specific variables must be defined within the configuration file. Once the variables have been defined, Adapter_Trimming can be submitted to a job scheduler with the following command (assuming that you are in the directory containing sequence_handling):

./sequence_handling Adapter_Trimming Config

Where Config is the full file path to the configuration file.

Handler-Specific Variables

The following are a list of variables that need to be defined within Config. In addition to the handler-specific variables, all common variables must be defined.

Variable	Function
AT_QSUB	QSub settings for batch submission. Recommended settings are "mem=1gb,nodes=1:ppn=8,walltime=10:00:00".
FORWARD_NAMING	Shared suffix for forward reads. If your files are named sample1_R1.fastq and sample2_R1.fastq, then FORWARD_NAMING=_R1.fastq
REVERSE_NAMING	Shared suffix for reverse reads. If your files are named sample1_R2.fastq and sample2_R2.fastq, then FORWARD_NAMING=_R2.fastq
ADAPTERS	A plain text or FastA file with the adapter sequences.
PRIOR	A prior contaminate estimate for Scythe. Scythe's documentation suggests starting at 0.05 and then experimenting as needed.

Note: If you have single-end samples, leave FORWARD_NAMING and REVERSE_NAMING filled with values that do NOT match your samples. If none of your samples match the forward or reverse naming suffixes, Adapter_Trimming will automatically assume that the samples are single-end.

Output

Adapter_Trimming creates a trimmed gzipped FastQ file for each sample. In addition, a list of all trimmed files will be output for use with other handlers. The full file path to this list will be

${OUT_DIR}/Adapter_Trimming/${PROJECT}_trimmed_adapters.txt

where ${OUT_DIR} and ${PROJECT} are specified in the configuration file.

After running Adapter_Trimming, there are three options for further processing.

1. Quality_Assessment can be used for more complete quality assurance.
2. Quality_Trimming can be used to trim low quality bases. This is generally not necessary when Read_Mapping with BWA-MEM. Future implementations of Read_Mapping using Bowtie 2 may require Quality_Trimming.
3. Read_Mapping can be used to map paired-end or GBS reads to a reference genome.

Dependencies

Adapter_Trimming depends on Scythe to perform the trimming. This is not installed on MSI and must be installed separately. Furthermore, PBS and GNU Parallel are required for operation.

Next: Quality_Trimming or Read_Mapping