Computational protocol: Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

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Protocol publication

[…] The raw reads of PE and MP libraries were trimmed for adapter sequence contamination and low-quality bases (PHRED score of FASTX-ToolKit (http://hannonlab.cshl.edu/fastx_toolkit/). The SOAPdenovo2 [] assembler was used to assemble all the high-quality PE and MP reads. The contigs were further scaffolded using SSPACE [] and gaps in the scaffolds were closed by GapCloser module in the SOAPdenovo2 []. The genome completeness of assembly was checked by CEGMA []. […]

Pipeline specifications

Software tools FASTX-Toolkit, SOAPdenovo, SSPACE, CEGMA
Application De novo sequencing analysis
Organisms Setaria italica, Oryza sativa
Chemicals Amino Acids, Calcium, Carbon, Methionine, Nitrogen, Tryptophan