{"doi":"10.21105/joss.06030","title":"Fasten: a toolkit for streaming operations on fastqfiles","abstract":"There are still many gaps in basic command line tools for the handling of standard file formats in the field of bioinformatics.Bioinformaticians have been able to use many tools to manipulate sequence data files in the fastq format, such as seqkit (Shen et al., 2016), seqtk (Li, 2023), FASTX-Toolkit (Gordon, 2014), seqfu (Telatin et al., 2021), jellyfish (Marcais & Kingsford, 2012), or BBTools (Bushnell, 2014).These tools only accept paired-end (PE) sequence data when split into multiple files per sample.Additionally, these tools do not always allow for Unix-style pipe file control.Sometimes they require explicitly input/output options instead of using stdin and stdout.However, some bioinformaticians prefer to combine PE data from a single sample into one file using the interleaved fastq file format, but this format is not always well supported in mainstream tools.Here, we provide Fasten to the community to address these needs.","journal":"The Journal of Open Source Software","year":2024,"id":494221,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9572,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":457042,"name":"John H. Phan","orcid":"0000-0002-4670-2660","position":1,"is_corresponding":false},{"id":788137,"name":"Henk C. den Bakker","orcid":"0000-0002-4086-1580","position":2,"is_corresponding":false},{"id":788138,"name":"Lee S. Katz","orcid":"0000-0002-2533-9161","position":0,"is_corresponding":true}],"reference_count":4,"raw_metadata":null,"created_at":"2026-07-19T02:09:07.920649Z","pmid":"39234029","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}