mikewolfe / bacterial_reseq Goto Github PK
View Code? Open in Web Editor NEWPipeline for processing bacterial re-sequencing data
Pipeline for processing bacterial re-sequencing data
Add rule to rename_breseq_output and update snakefile to know about it
Change line 32 in quality_control.smk from
out = lookup_sample_metadata(sample, "file_path", pep)
to
out = lookup_sample_metadata(sample, "infile_path", pep)
"infile_path" is the name of the column in the sample sheet, not "file_path"
Although breseq
is a great tool, it is not designed to deal with large changes containing exogenous DNA not found in the reference. To quote the breseq
methods paper (https://doi.org/10.1007/978-1-4939-0554-6_12):
The re-sequencing strategy employed by breseq breaks down when there is sufficient sequence divergence between the sample and the reference genome to lead to mismapping of reads, such as when there is a high level of local nucleotide divergence or there are novel sequences in the sample that are not in the reference genome. In these cases, it may be valuable to use de novo assembly tools, such as Velvet (10.1101/gr.074492.107) or ALLPATHS-LG (10.1101/gr.141515.112), on either the unmapped reads after a breseq run (located at data/unmatched.*) or all reads and then compare assemblies to the reference genome or to one another using tools for comparing whole-genome sequences, such as MUMmer (10.1186/gb-2004-5-2-r12).
I think we should follow their suggestion and use these tools to perform a de-novo assembly of the sequencing samples.
conda
installable (i.e. MUMmer is https://anaconda.org/bioconda/mummer)workflow/rules/denovo_assembly.smk
to run the assemblyConsumers would like a BAM file to scrutinize for each sample. General parameters for alignment should be fine.
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