ArticleBioinformatics (Oxford, England)2024
Flexible parsing, interpretation, and editing of technical sequences with splitcode.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.Bioinformatics (Oxford, England) · 2026Article
- ReadChop: a high-performance demultiplexer for long-read sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Long-read sequencing transcriptome quantification with lr-kallisto.PLoS computational biology · 2025Article
- Synthbar: A Lightweight Tool for Adding Synthetic Barcodes to Sequencing Reads.bioRxiv : the preprint server for biology · 2025Article
- Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.Nucleic acids research · 2025Article
- Flexiplex: a versatile demultiplexer and search tool for omics data.Bioinformatics (Oxford, England) · 2024Article
- kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.bioRxiv : the preprint server for biology · 2024Article
- simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry.Bioinformatics (Oxford, England) · 2023Article
- simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry.bioRxiv : the preprint server for biology · 2023Article
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2 authors.
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Abstract
motivationNext-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences can be essential for interpreting results of sequencing assays, and when they contain information pertinent to an experiment, they must be processed and analyzed.
resultsWe present a tool called splitcode, that enables flexible and efficient parsing, interpreting, and editing of sequencing reads. This versatile tool facilitates simple, reproducible preprocessing of reads from libraries constructed for a large array of single-cell and bulk sequencing assays. AVAILABILITY AND IMPLEMENTATION: The splitcode program is available at http://github.com/pachterlab/splitcode.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.