pvphaneuf / seqpostproc Goto Github PK

Summarize # of mutations, coverage of samples, etc, in a CSV file.

Upfront, the # of mutations for each same will be valuable to know which sample reseq's are potentially problematic.

1. breseq
2. fastx
3. trim_galore
4. cut adapt
5. fastqc

We want to grab the HTML annotation for the mutation annotation and sequence change info from the GD file output by gdtools ANNOTATE rather than by parsing the HTML breseq report.

Trying to avoid scraping/parsing HTML when possible.

Constantly getting issues with read file names causing auto-grouping of file names to malfunction. Should instead simply have CSV input file that describes all of the files to Breseq and the name of the output.

According to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103590/, Trimmomatic give best alignment after adapter and quality trimming. Trimmomatic differs from trim_galore(Cutadapt) in that it uses a sliding window quality trimmer, which generally give better results than other quality trimming approaches.

Questions that need to be answered before substituting trimming software, where trim_galore currently accomplishes these tasks:

• Does Trimmomatic automatically detect adapter sequences?

1. adapter trimming
2. quality trimming
3. resequencing

It is deleting the distribution data for reads. Rather, write this steps to know the specific folders that need to be deleted from each report.