Commands ======== Five commands move reads, and three read no reads at all. That count is fixed: a sixth pipeline command needs a failing benchmark that the existing five cannot pass, because every flag and every stage is a thing that can disagree with another one. The pipeline ------------ .. code-block:: bash migec checkout reads.fq.gz --bc-pattern '^NNNNNNNN' -o co/ # find and cut out the barcode migec refine co/S1.fq.gz -o ref/ # fix the errors IN the barcode migec assemble ref/S1.fq.gz -o asm/ # collapse each molecule .. list-table:: :header-rows: 1 :widths: 18 34 48 * - command - what it does - the number it decides * - :doc:`suggest ` - reads the barcode layout off the data - the pattern you paste into ``checkout`` * - :doc:`checkout ` - finds the pattern, cuts the barcode out, demultiplexes - how many reads carry a usable barcode * - :doc:`refine ` - corrects errors in the barcode itself, calls cells - **how many molecules there were** * - :doc:`assemble ` - collapses each molecule's reads into one consensus - the sequence, and the quality it is allowed to claim * - :doc:`subsample ` - keeps every read of a fraction of the barcodes - how many molecules a smaller copy of the library holds ``suggest`` and ``subsample`` are outside the pipeline in different directions: one runs before it to tell you what to type, the other cuts a library down to something a laptop can iterate on. Reading the output ------------------ .. list-table:: :header-rows: 1 :widths: 18 34 48 * - command - what it does - reads no reads because * - :doc:`plot ` - draws twenty QC panels from the TSVs the stages wrote - it computes nothing; a figure that cannot be redrawn from a committed table will eventually disagree with the report * - ``sheet`` - writes or explains a barcode table, lists the presets - it only ever touches the layout * - ``info`` - prints what a ``.mig`` bucket or a tagged FASTQ contains - it reads headers Every stage writes plain TSV next to its output and a ``.json`` summary beside that, so the :doc:`figures ` and any downstream script see the same numbers the report printed. .. toctree:: :maxdepth: 1 suggest checkout refine assemble subsample plots