Removes residual adapter sequences from the ends of single-end or paired-end unmerged FASTQ reads that may remain after trimming with tools like fastp. The program targets only previously untrimmed reads (i.e., reads with full sequencing cycle length), scans the bases at the 3' end for adapter sequences, and trims them even if only a single base matches the adapter.
- A C++ compiler with C++17 support
- zlib library
Run the following commands:
git clone https://github.com/bilalbioinfo/AdaptClean.git
cd AdaptClean
makeBy default make will compile the program and install the AdaptClean binary to /bin.
AdaptClean <input.fastq[.gz]> <output.fastq[.gz]> <sequencing_cycle_length> <adapter_sequence>
Example:
AdaptClean reads.fastq.gz reads.trimmed.fastq.gz 75 AGATCNotes:
- Input is treated as gzipped only if the filename ends with
.gz. - Trimming is applied only to reads whose length equals the given sequencing cycle.
Contact: Bilal Sharif bilal.bioinfo@gmail.com