fastp - MOSHPIT documentation

Plugin Overview¶

QIIME 2 plugin for sequence processing with fastp.

version: 2026.4.0
website: https://github.com/bokulich-lab/q2-fastp
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
process-seqs	method	Process sequences with fastp.
collate-fastp-reports	method	Collate fastp reports.
visualize	visualizer	Visualize the fastp reports.

Artifact Classes¶

FastpJSONReports

Formats¶

FastpJsonFormat

FastpJsonDirectoryFormat

fastp process-seqs¶

Uses fastp to process input sequences with various quality control options.

Citations¶

Chen, 2023

Inputs¶

sequences: SampleData[SequencesWithQuality] | SampleData[PairedEndSequencesWithQuality]: Input sequences.[required]

Parameters¶

trim_front1: Int % Range(0, None): Number of bases to trim from the front of forward read.[default: 0]
trim_tail1: Int % Range(0, None): Number of bases to trim from the tail of forward read.[default: 0]
max_len1: Int % Range(0, None): If forward read is longer than max_len1, then trim it at its tail to make it as long as max_len1[default: 0]
trim_front2: Int % Range(0, None): Number of bases to trim from the front of reverse read.[default: 0]
trim_tail2: Int % Range(0, None): Number of bases to trim from the tail of reverse read.[default: 0]
max_len2: Int % Range(0, None): If reverse read is longer than max_len2, then trim it at its tail to make it as long as max_len2[default: 0]
disable_quality_filtering: Bool: Disable quality filtering.[default: False]
n_base_limit: Int % Range(0, None): The maximum number of N bases allowed in a read.[default: 5]
qualified_quality_phred: Int % Range(0, None): The quality value that a base is qualified.[default: 15]
unqualified_percent_limit: Int % Range(0, 100): The maximum percentage of unqualified bases allowed in a read.[default: 40]
length_required: Int % Range(0, None): The minimum length required for a read to be kept.[default: 15]
compression: Int % Range(1, 12): The compression level for the output files.[default: 2]
thread: Int % Range(1, None): The number of threads to use.[default: 1]
dedup: Bool: Enable duplication removal.[default: False]
dup_calc_accuracy: Int % Range(0, 6, inclusive_end=True): The accuracy for duplication calculation.[default: 3]
dont_eval_duplication: Bool: Disable duplication evaluation.[default: False]
disable_adapter_trimming: Bool: Disable adapter trimming.[default: False]
adapter_sequence: Str: The adapter sequence for read 1.[default: '']
adapter_sequence_r2: Str: The adapter sequence for read 2.[default: '']
poly_g_min_len: Int % Range(0, None): The minimum length of polyG tail to be detected.[default: 10]
poly_x_min_len: Int % Range(0, None): The minimum length of polyX tail to be detected.[default: 10]
overlap_len_require: Int % Range(0, None): The minimum length to detect overlapped region of PE reads.[default: 30]
overlap_diff_limit: Int % Range(0, None): The maximum number of mismatched bases to detect overlapped region of PE reads.[default: 5]
overlap_diff_percent_limit: Int % Range(0, 100): The maximum percentage of mismatched bases to detect overlapped region of PE reads.[default: 20]
correction: Bool: Enable base correction in overlapped regions.[default: False]
cut_window_size: Int % Range(1, None): The window size option shared by cut_front, cut_tail or cut_sliding.[default: 4]
cut_mean_quality: Int % Range(1, 36): The mean quality requirement option shared by cut_front, cut_tail or cut_sliding.[default: 20]
cut_front: Bool: Move a sliding window from front (5') to tail.[default: False]
cut_tail: Bool: Move a sliding window from tail (3') to front.[default: False]
cut_right: Bool: Move a sliding window from front to tail.[default: False]
overrepresentation_analysis: Bool: Enable overrepresentation analysis.[default: False]
overrepresentation_sampling: Int % Range(0, 10000): The sampling number for overrepresentation analysis. Smaller is slower.[default: 20]

Outputs¶

processed_sequences: SampleData[SequencesWithQuality] | SampleData[PairedEndSequencesWithQuality]: Sequences processed by fastp.[required]
reports: FastpJSONReports: Fastp JSON reports.[required]

fastp collate-fastp-reports¶

Collate fastp reports into a single artifact.

Inputs¶

reports: List[FastpJSONReports]: <no description>[required]

Outputs¶

collated_reports: FastpJSONReports: <no description>[required]

fastp visualize¶

Generate a MultiQC visualization of the JSON reports generated by fastp.

Citations¶

Ewels et al., 2016

Inputs¶

reports: FastpJSONReports: Fastp JSON reports.[required]

Outputs¶

visualization: Visualization: <no description>[required]

References¶

Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107
Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. 10.1093/bioinformatics/btw354