Computational protocol: Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors

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Protocol publication

[…] For the reference genome, Illumina genomic reads from two libraries were filtered and assembled with AllPathsLG (Gnerre et al., ). RNA-seq data for each genome were de novo assembled into consensus sequences using Rnnotator (Martin et al., ). The genome assembly was annotated using the JGI Annotation Pipeline and made available via the JGI fungal genome portal MycoCosm (jgi.doe.gov/fungi; Grigoriev et al., ). The Whole Genome Shotgun project of the reference isolate CCP has been deposited at DDBJ/ENA/GenBank under the accession NSJI00000000. The version described in this paper is version NSJI01000000.For additional strains, after quality control, short reads were assembled in contigs using Velvet v.1.2.10 (Zerbino and Birney, ) with k-mers hash tables of 57 and automatic coverage cutoff. Mapping back the short reads to the generated contigs validated assembly parameters, yielding >97% mapped and >90% properly paired reads with the BWA SAMPE algorithm (Li and Durbin, ).Post-assembly/annotation analysis relied on a parallel implementation (Tange, ) hosted by an Ubuntu 12.10 x64 server running on a 32-thread Intel Xeon Dell PowerEdge R720 server.The Whole Genome Shotgun project of the additional C. cassiicola strains (BioProject PRJNA428435) has been deposited at DDBJ/ENA/GenBank under the accessions POQW00000000 to POSE00000000. The versions described in this paper are versions POQW01000000 to POSE01000000. […]

Pipeline specifications

Software tools Rnnotator, Velvet, BWA
Databases DDBJ MycoCosm
Application RNA-seq analysis
Organisms Homo sapiens, Fungi, Colletotrichum acutatum, Fusarium oxysporum