FastGT: from raw sequence reads to 30 million genotypes in less than an hour
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منابع مشابه
RNA-seq data comparisons of wild soybean genotypes in response to soybean cyst nematode (Heterodera glycines)
Soybean [Glycine max (L.) Merr.] is an important crop rich in vegetable protein and oil, and is a staple food for human and animals worldwide. However, soybean plants have been challenged by soybean cyst nematode (SCN, Heterodera glycines), one of the most damaging pests found in soybean fields. Applying SCN-resistant cultivars is the most efficient and environmentally friendly strategy to mana...
متن کاملDe novo Assembly and Characterization of Cajanus scarabaeoides (L.) Thouars Transcriptome by Paired-End Sequencing
Pigeonpea [Cajanus cajan (L.) Millsp.] is a heat and drought resilient legume crop grown mostly in Asia and Africa. Pigeonpea is affected by various biotic (diseases and insect pests) and abiotic stresses (salinity and water logging) which limit the yield potential of this crop. However, resistance to all these constraints is not readily available in the cultivated genotypes and some of the wil...
متن کاملTopHat: discovering splice junctions with RNA-Seq
MOTIVATION A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or 'reads', can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify no...
متن کاملGINDEL: Accurate Genotype Calling of Insertions and Deletions from Low Coverage Population Sequence Reads
Insertions and deletions (indels) are important types of structural variations. Obtaining accurate genotypes of indels may facilitate further genetic study. There are a few existing methods for calling indel genotypes from sequence reads. However, none of these tools can accurately call indel genotypes for indels of all lengths, especially for low coverage sequence data. In this paper, we prese...
متن کاملTranscriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom)
Elettaria cardamomum (L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild...
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