From e8708308704182d54874aecd2d6cfa99ddbe820d Mon Sep 17 00:00:00 2001 From: Minh Duc Cao Date: Mon, 26 Sep 2016 12:51:31 +1000 Subject: [PATCH] update cite --- README.rst | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 4dea5a7..cc6c13c 100644 --- a/README.rst +++ b/README.rst @@ -10,9 +10,8 @@ of Oxford Nanopore sequencing data, as described in the paper: Streaming algorithms to identify pathogens and antibiotic resistance potential from real-time MinION sequencing -Minh Duc Cao, Devika Ganesamoorthy, Alysha Elliott, Huihui Zhang, Matthew Cooper, Lachlan Coin +Cao, M. D., Ganesamoorthy, D., Elliott, A. G., Zhang, H., Cooper, M. A., & Coin, L. J. M. (2016). Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing. GigaScience, 5(1), 32. http://doi.org/10.1186/s13742-016-0137-2 -(To appear in GigaScience, a preprint of the article can be found on bioRxiv server at doi: http://dx.doi.org/10.1101/019356) ===================== Software installation @@ -202,7 +201,7 @@ In these sub-pipelines, you may want to modify the parameter -port for jsa.util Once these `daemons `_ are ready for their analyses, you can start npReader to streamline data into the integrated pipeline:: - jsa.np.f5reader -GUI -realtime -folder -fail -output data.fastq -stream server1:port1,server2:port2,server3:port3 + jsa.np.npreader -GUI -realtime -folder -fail -output data.fastq -stream server1:port1,server2:port2,server3:port3 in which the -folder parameter specifies the downloads folder from the Metrichor base-calling, and the -stream parameter lists the computer addresses and port numbers that the analyses are listening on. At this point, you can start the MinION and Metrichor to start the real-time analyse. @@ -210,6 +209,8 @@ in which the -folder parameter specifies the downloads folder from the Metrichor Retro-realtime analysis ======================= +Note npreader no longer support extracting time information. Please use an earlier version for this. + If your data have been sequenced, and depending on what processing steps have been done. * If your data have not been base-cased, you can start the pipeline as above, and run Metrichor for base-calling your data. @@ -222,7 +223,7 @@ If your data have been sequenced, and depending on what processing steps have be * If you want to emulate the timing of your sequenced data, first convert the data to fastq format and extract the timing information (make sure parameter -time is turned on):: - jsa.np.f5reader -folder -fail -number -stat -time -out dataT.fastq + jsa.np.npreader -folder -fail -number -stat -time -out dataT.fastq Next sort the reads in the order they were generated:: @@ -256,7 +257,7 @@ Further documentations More details of usage of the discussed programs are provided in `ReadTheDocs for Japsa `_. More specificially: -* `npReader `_ +* `npReader `_ * `jsa.util.streamServer `_ * `jsa.util.streamClient `_ * `jsa.np.filter `_