Difference: ProtocolsFlexbarCommands (11 vs. 12)

Revision 122014-08-12 - DanielDeatherage

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META TOPICPARENT name="ProtocolList"

Using Flexbar program to remove adapter sequences from NGS reads

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Command line usage for removal of adapter sequences

The following does not apply to standard illumina sequencing libraries including MiSeq runs. DNAzyme project (this involved constant non-informative regions flanking each side of a library) revealed unexpected flexbar behavior. Specifically both the left and right ends of a single sequence can not be modified in a single pass. All "adapter" sequences are aligned to each read at once, and the sequence with the best alignment is acted on. This means that in a single pass only the left or right adapter can be trimmed. To avoid this recommend that 2 passes are performed: left, then right.
 Generic command for performing maximal (aggressive) trimming. Replace everything between "" with appropriate names, and delete the "" marks:

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

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