diff --git a/README.md b/README.md index bd8e6567..a7f4a639 100644 --- a/README.md +++ b/README.md @@ -104,6 +104,9 @@ The following comments refer to the filters that are explained in the FAQ above. CCS below minimum RQ : 0 (0.00%) <- Predicted accuracy is below --min-rq (5) Unknown error : 0 (0.00%) <- Rare implementation errors +If run in `--by-strand` mode, rows may contain half ZMWs, as we account +each strand as half a ZMW. + ### What is the definition of a heteroduplex? In general, whenever bases on one strand of the SMRTbell are not the reverse complement of the other strand, as small as a single base `A` with a @@ -201,7 +204,8 @@ cp /some/download/dir/model.json "${SMRT_CHEMISTRY_BUNDLE_DIR}"/arrow/ ### How fast is CCS? We tested CCS runtime using 1,000 ZMWs per length bin with exactly 10 passes. - + + #### How does that translate into time to result per SMRT Cell? We will measure time to result for Sequel I and II CCS sequencing collections @@ -274,6 +278,15 @@ Read name suffix indicates strand. Example: m64011_190714_120746/14/ccs/rev m64011_190714_120746/35/ccs/fwd +How does `--by-strand` work? For each ZMW: + * Determine orientation of reads with respect to the one closest to the mean length + * Sort reads into two buckets, forward and reverse strands + * Treat each strand as an individual entity as we do with ZMWs + * Apply all filters per strand individually + * Create a draft for each strand + * Polish each strand + * Write out each polished strand consensus + ### Is there a progress report? Yes. With `--log-level INFO`, _ccs_ provides status to `stderr` every `--refresh-rate seconds` (default 30): @@ -315,10 +328,16 @@ and statically links GNU C Library v2.29 licensed under [LGPL](https://spdx.org/ Per LPGL 2.1 subsection 6c, you are entitled to request the complete machine-readable work that uses glibc in object code. + ## Changelog - * **4.0.0**: - * SMRT Link v8.0 release candidate + * **4.1.0**: + * Minor speed improvements + * Fix `--by-strand` logic, see more [here](#can-i-produce-one-consensus-sequence-for-each-strand-of-a-molecule) + * Allow vanilla `.xml` output without specifying dataset type + * Compute wall start/end for each output read (future basecaller functionality) + * 4.0.0: + * SMRT Link v8.0 release * Speed improvements * Removed support for legacy python Genomic Consensus, please use [gcpp](https://github.com/PacificBiosciences/gcpp) * New command-line interface diff --git a/img/runtime.png b/img/runtime.png index 63492414..00768e30 100644 Binary files a/img/runtime.png and b/img/runtime.png differ