ArticleBioinformatics (Oxford, England)2010
inGAP: an integrated next-generation genome analysis pipeline.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies.Biomedicines · 2025Article
- inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities.Genomics, proteomics & bioinformatics · 2022Article
- Development and Evaluation of a Point-of-Care Test in a Low-Resource Setting with High Rates of Chlamydia trachomatis Urogenital Infections in Fiji.Journal of clinical microbiology · 2021Article
- The synaptonemal complex imposes crossover interference and heterochiasmy inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Correlation of drug resistance with single nucleotide variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M. tuberculosis.BMC microbiology · 2020Article
- Resequencing of the Red Alga Cyanidioschyzon merolae: Strain Differences and Mitochondrial Sequence Corrections.Microbiology resource announcements · 2020Article
- The cohesin loader SCC2 contains a PHD finger that is required for meiosis in land plants.PLoS genetics · 2020Article
- Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.Nucleic acids research · 2019Article
- Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.BioMed research international · 2019Review
- A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data.Computational and structural biotechnology journal · 2018Review
- Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed.Nature communications · 2017Article
- A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes.Genome biology · 2016Article
- SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.BMC bioinformatics · 2016Article
- BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection.Nucleic acids research · 2015Article
- Phylogenomics of non-model ciliates based on transcriptomic analyses.Protein & cell · 2015Article
- Saccharina genomes provide novel insight into kelp biology.Nature communications · 2015Article
- Spontaneous dominant mutations in chlamydomonas highlight ongoing evolution by gene diversification.The Plant cell · 2015Article
- CIRI: an efficient and unbiased algorithm for de novo circular RNA identification.Genome biology · 2015Article
- Assembling flagella in Salmonella mutant strains producing a type III export apparatus without FliO.Journal of bacteriology · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryWe develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length. Experiments on simulated and experimental data show that this pipeline can achieve overall 97% accuracy in SNP detection and 94% in the finding of indels. All the detected SNPs/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly. AVAILABILITY: inGAP is available at http://sites.google.com/site/nextgengenomics/ingap
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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.