Using Flexbar program to remove adapter sequences from NGS reads

Installing Flexbar

installation instructions coming soon.

Command line usage for removal of adapter sequences

Generic conservative command. Replace everything between "" with appropriate names, and delete the "" marks:

flexbar -t "New_file_name" -s "read_1_file_name" -p "read_2_file_name" -f fastq -a "fasta_file_of_adapter_sequences" -ao 1

Example command:

flexbar -t DED81 -s 02_Downloads/Sample_DED81_L004_R1.cat.fastq -p 02_Downloads/Sample_DED81_L004_R2.cat.fastq -f fastq -a 02_trimmed_Downloads/adapter_seq.fasta -ao 1

For a less conservative command, remove -ao 1

Flag explanations

Flag	Text to follow	What flag means	Reason
-t	New_file_name	Name of output file.	Dictate what your output file is to be named. Suggest something different than input to avoid overwriting untrimmed.
-s	R1_source_file_name	Name of Read1 sequencing file.	File to remove adapters from.
-p	R2_source_file_name	Name of Read2 sequencing file.	File to remove adapters from.
-f	Format	Format of reads.	Most commonly will be fasta or fastq.
-a	Adapter_sequence_file.fasta	Fasta file with full adapter sequences, degenerate bases allowed.	What sequence is to be removed.
-ao	Number	Number of bases of overlap between read and adapter	This number equals the minimum number of bp to be removed.
-at	Number	Number of mismatches and indels per 10bp of adapter sequence allowed	This accounts for sequencing/PCR errors changing adapter sequence. Default = 3, increasing this number increases false positive rate, and decreases false negative rate.

Additional Information

For additional information, type flexbar -h -- Main.DanielDeatherage - 16 Jan 2013