From second generation sequencing reads to nucleotide counts This small pipeline works with single illumina reads (no PE).
make all
- You may want to run
make qcfirst and use its results to tweak the trimming parameters - By default the TrueSeq3 adapters will be trimmed by Trimmomamtic
- Python + Biopython
- FastQC
- Kraken
- Trimmomatic
- kallisto
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