Ichthyophonus de novo (Fish 546)

This record includes files that resulted from de novo assembly of short read (Illumina PE100) genomic data from the parasite Ichthyophonus.  I would like to acknowledge K. Nichols for supplying the data for this analysis.

Files included in this data set:

Ichthlyophonus de novo (Fish546).pdf; Presentation giving overview of project and summary results.

AssemblyParameters.pdf; Software settings for CLC and SOAPdenovo assemblers.

11186ContigSummary.csv; Tablular data for contig length and coverage from CLC assembly.

SoapContigSummary.csv; Tabular data for contig length and coverage from SOAPdenovo assembly.

CLC_Choanoflagellate_Blast_GO_Annot...csv; Blast results from annotated Choanoflagellate genome query on Ichthyophonus contig database from CLC.  File is a merger of blast results and annotation table.

CLC_Fungi_Blast_GO_Annotations.csv; Blast results from annotated Fungal genome query on Ichthyophonus contig database from CLC. File is a merger of blast results and annotation table.

CLC_Metazoa_Blast_GO_Annotations.csv; Blast results from annotated Metazoan genome query on Ichthyophonus contig database from CLC. File is a merger of blast results and annotation table.

SOAP_Choanoflagellate_Blast_GO_Anno...csv; Blast results from annotated Choanoflagellate genome query on Ichthyophonus contig database from SOAP. File is a merger of blast results and annotation table.

SOAP_Fungi_Blast_GO_Annotations.csv; Blast results from annotated Fungal genome query on Ichthyophonus contig database from SOAP. File is a merger of blast results and annotation table.

SOAP_Metazoan_Blast_GO_Annotations.csv; Blast results from annotated Metazoan genome query on Ichthyophonus contig database from SOAP. File is a merger of blast results and annotation table.

CLC_OpenReadingFrames.bed; Bed file with putative Open Reading Frames from the CLC assembly, produced by EMBOSS "getorf" funcion, implemented in Galaxy.

SNP_RestrictionBed.bed; Bed file with putative SNP sites, produce by converting .gff SNP file from CLC assembly.

Choanoflagellate_Blast.bed; Bed file of Choanoflagellate blast hits, converted from CLC blast output file above.

Fungi_Blast.bed; Bed file of Fungal blast hits, converted from CLC blast output above.

Metazoa_Blast.bed; Bed file of Metazoan blast hits, converted from CLC blast output above.

igv_snapshot.png; Example of blast hits, SNPs and restriction enzyme sites displayed in Integrated Genomic Viewer.