fastp(1) on Linux
The text e167c07d6852, as Debian 11 (Bullseye) shipped it.
ultra-fast all-in-one FASTQ preprocessor
Flags it lists
-
--adapter_fasta -
--adapter_sequence -
--adapter_sequence_r2 -
--average_qual -
--complexity_threshold -
--compression -
--correction -
--cut_by_quality3 -
--cut_by_quality5 -
--cut_by_quality_aggressive -
--cut_front -
--cut_front_mean_quality -
--cut_front_window_size -
--cut_mean_quality -
--cut_right -
--cut_right_mean_quality -
--cut_right_window_size -
--cut_tail -
--cut_tail_mean_quality -
--cut_tail_window_size -
--cut_window_size -
--detect_adapter_for_pe -
--disable_adapter_trimming -
--disable_length_filtering -
--disable_quality_filtering -
--disable_trim_poly_g -
--discard_unmerged -
--dont_overwrite -
--failed_out -
--filter_by_index1 -
--filter_by_index2 -
--filter_by_index_threshold -
--fix_mgi_id -
--help -
--html -
--in1 -
--in2 -
--include_unmerged -
--interleaved_in -
--json -
--length_limit -
--length_required -
--low_complexity_filter -
--max_len1 -
--max_len2 -
--merge -
--merged_out -
--n_base_limit -
--out1 -
--out2 -
--overlap_diff_limit -
--overlap_diff_percent_limit -
--overlap_len_require -
--overrepresentation_analysis -
--overrepresentation_sampling -
--phred64 -
--poly_g_min_len -
--poly_x_min_len -
--qualified_quality_phred -
--reads_to_process -
--report_title -
--split -
--split_by_lines -
--split_prefix_digits -
--stdin -
--stdout -
--thread -
--trim_front1 -
--trim_front2 -
--trim_poly_g -
--trim_poly_x -
--trim_tail1 -
--trim_tail2 -
--umi -
--umi_len -
--umi_loc -
--umi_prefix -
--umi_skip -
--unpaired1 -
--unpaired2 -
--unqualified_percent_limit -
--verbose -
-3 -
-5 -
-6 -
-? -
-A -
-B -
-F -
-G -
-I -
-L -
-M -
-O -
-P -
-Q -
-R -
-S -
-T -
-U -
-V -
-W -
-Y -
-a -
-b -
-c -
-d -
-e -
-f -
-g -
-h -
-i -
-j -
-l -
-m -
-n -
-o -
-p -
-q -
-r -
-s -
-t -
-u -
-w -
-x -
-y -
-z