Usage of `art_profile_builder`¶

This new executable is designed to suppress the old art_profiler_illumina Shell/Perl scripts for building ART-compatible quality profiles. It supports building profiles from FASTQ and SAM/BAM files. Added in 1.1.9.

NOTE For MPI users: Currently, this executable runs under one slot (mpiexec -n 1) only. If more than one slot is provided, processes with MPI rank larger than 0 will terminate themselves.

Options¶

--i-file: Input file path. FASTQ/SAM/BAM files are supported. We currently rely on HTSLib to determine file format automatically. See also: htsfile(1).
--i-num_threads: Number of threads used to decompress input.
--i-format: Input file format. Added in 1.3.4. NOTE Must specify the format if reading from irregular files, like /dev/stdin.
--first_n_reads: Number of reads to use.
--read_len: Read length. For each read, only the first read_len bases are used. If the read is shorter than read_len, only the available bases are used.
--read_len_1 and --read_len_2: Read lengths for read 1 and read 2 respectively. They cannot be used together with --read_len.
--is_pe: For SAM/BAM input, set if the input is paired-end.
--o-file1: Output quality profile file path for read 1.
--o-file2: Output quality profile file path for read 2. Required if --is_pe is set.
--parallel: Same as art_modern’s --parallel.
--old_behavior: Simulate the behavior of original ART profile builder. If set, all qualities will be offset by 1. See also: The Bug in Srcurity.md.

Environment Variables¶

Same as art_modern’s environment variables.

Notes¶

The input SAM/BAM files does NOT need to be sorted.
For input SAM/BAM files, only reads with quality will be used to build the profile. So, if you would build the profile using aligned SAM/BAM files, to ensure that all reads will be used, please make sure that:
- Unaligned reads are included in the input SAM/BAM file;
- All primary- and unaligned reads have quality information;
- Secondary- or supplementary-aligned reads have no quality information.
Automatic format detection is supported. However:
- If the input file is not a regular file, --i-format must be specified.
- The program will firstly try to detect SRA format if supported. If not, the program will try to tell format using HTSLib. See also: htsfile(1).

Example¶

Building profiles from single-end FASTQ files:

art_profile_builder \
    --i-file out_se.fq \
    --read_len 36 \
    --o-file1 out_se_art_cxx_fq.txt \
    --parallel 2 \
    --i-num_threads 4

Building profiles from paired-end FASTQ files:

for i in 1 2; do
    art_profile_builder \
        --i-file out_pe."${i}".fq \
        --read_len 36 \
        --o-file1 out_pe_art_cxx_fq_R"${i}".txt \
        --parallel 2 \
        --i-num_threads 4
done

Building profiles from single-end SAM/BAM files:

art_profile_builder \
    --i-file out_se.sam \
    --read_len 36 \
    --o-file1 out_se_art_cxx_sam.txt \
    --parallel 2 \
    --i-num_threads 4

Building profiles from paired-end SAM/BAM files:

art_profile_builder \
    --i-file out_pe.sam \
    --read_len 36 \
    --is_pe \
    --o-file1 out_pe_art_cxx_sam_R1.txt \
    --o-file2 out_pe_art_cxx_sam_R2.txt \
    --parallel 2 \
    --i-num_threads 4

Building profiles from paired-end SRA files:

art_profile_builder \
    --i-file out_pe.sra \
    --read_len 36 \
    --is_pe \
    --o-file1 out_pe_art_cxx_sra_R1.txt \
    --o-file2 out_pe_art_cxx_sra_R2.txt \
    --parallel 2 \
    --old_behavior

Usage of art_profile_builder¶

Options¶

Environment Variables¶

Notes¶

Example¶

Usage of `art_profile_builder`¶