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Jenna M. Lang edited Genome Assembly and Annotation.md
almost 10 years ago
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/Applications/a5_pipeline/bin/a5_pipeline.pl SequenceFile1.fastq SequenceFile2.fastq MyGenome
Once the program finishes running you will have a complete assembly located in the a5\_output folder.
Among the numerous files generated by A5, two of particular importance are the "MyGenome.contigs.fasta" and "MyGenome.final.scaffolds.fasta" which contain the contigs and scaffolds, respectively.
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Finally "X\_cov" shows the average coverage across the genome. For Illumina data we recommend that this number be between ~30X and 100X. Much less than 30X coverage and the quality of any given base in the assembly may come into question. Conversely, too much coverage can reduce the quality of the assembly and require downsampling. **Instructions or reference for downsampling?**
###Verification of 16S Sequence
Follow the steps described in Section ??, "Making a Phylogenetic Tree" for obtaining and
BLASTing performing a BLAST search of the full length 16s sequence.
PhyloSift
Navigate to