ArticleFrontiers in immunology2012
Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing.
Article in Frontiers in immunology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Mutational patterns along different evolution paths of follicular lymphoma.Frontiers in oncology · 2022Article
- Gastric DLBCL clonal evolution as function of patient age.Frontiers in immunology · 2022Article
- VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.BMC bioinformatics · 2017Article
- Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children.Nature communications · 2017Article
- Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults.Frontiers in immunology · 2016Article
- Complexity of the human memory B-cell compartment is determined by the versatility of clonal diversification in germinal centers.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The evolution and development of the antibody repertoire.Frontiers in immunology · 2015Article
- Old questions, new tools: does next-generation sequencing hold the key to unraveling intestinal B-cell responses?Mucosal immunology · 2015Review
- The promise and challenge of high-throughput sequencing of the antibody repertoire.Nature biotechnology · 2014Review
- Immunoglobulin gene repertoire diversification and selection in the stomach - from gastritis to gastric lymphomas.Frontiers in immunology · 2014Article
- Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template.Journal of clinical bioinformatics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing (HTS) yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig) genes, which are variable and often highly mutated. This paper describes Ig High-Throughput Sequencing Cleaner (Ig-HTS-Cleaner), a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig Insertion-Deletion Identifier (Ig-Indel-Identifier), a program for identifying legitimate and artifact insertions and/or deletions (indels). Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.
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Registered trials
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.