Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool
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Summary
PyroCleaner is a software module intended to clean 454 pyrosequencing reads in order to ease the assembly process and includes commonly used filters as well as specialised ones such as duplicated read removal and paired-end read verification.
- Type
- article
- Published
- 2011-05-26
- Cited by
- 55
- References
- 8
- Access
- Open access
- OpenAlex
- https://openalex.org/W2011637810
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:15690138
Keywords
Pyrosequencing, Computer science, MIT License, Python (programming language), Replicate
References
- DNA sequence quality trimming and vector removal
- Systematic artifacts in metagenomes from complex microbial communities
- A Greedy Algorithm for Aligning DNA Sequences
- Base-calling of automated sequencer traces using phred. II. Error probabilities.
- Figaro: a novel statistical method for vector sequence removal
- Artificial and natural duplicates in pyrosequencing reads of metagenomic data
Cited by
- Intra-host viral variability in children clinically infected with H1N1 (2009) pandemic influenza.
- Characteristics of Pyrosequencing Data – Analysis, Methods, and Tools
- Plasticité phénotypique et architecture génétique de la croissance et de la densité du bois du pin maritime (Pinus pinaster Ait.)
- Mise en évidence de la synténie de QTL de tolérance au gel sur les groupes de liaison VI chez Pisum sativum (WFD 6.1) et Medicago truncatula (Mt-FTQTL6) et cartographie fine de Mt-FTQTL6
- Deciphering HIV genetic variability and evolution by massive parallel pyrosequencing and bioinformatics
- Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods
- Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data—The Case of the Grass Aegilops tauschii Complex Genome
- High‐density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)
- NG6: Integrated next generation sequencing storage and processing environment
- Analysis of plant microbe interactions in the era of next generation sequencing technologies
- Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection
- Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
- Teleost Fish Mount Complex Clonal IgM and IgT Responses in Spleen upon Systemic Viral Infection
- A tandem array of CBF/DREB1 genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6
- Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea
- Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail
- First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta).
- The Highly Prolific Phenotype of Lacaune Sheep Is Associated with an Ectopic Expression of the B4GALNT2 Gene within the Ovary
- Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress
- Comparative analysis of mitochondrial genomes of Rhizophagus irregularis - syn. Glomus irregulare - reveals a polymorphism induced by variability generating elements.
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