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