From 20d3cff7d7f483bd779aff75f861e93708c0a2b5 Mon Sep 17 00:00:00 2001 From: Vince Buffalo Date: Fri, 17 Oct 2014 14:11:49 -0700 Subject: [PATCH] fixed error in readme, thanks to @kbradnam --- README.md | 8 ++++---- src/scythe.c | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index d17ae47..7bf9915 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Scythe - A Bayesian adapter trimmer (version 0.993 BETA) +# Scythe - A Bayesian adapter trimmer (version 0.994 BETA) Scythe and all supporting documentation Copyright (c) Vince Buffalo, 2011-2014 @@ -69,18 +69,18 @@ If you'd like to use standard out, it is recommended you use the Also, more detailed output about matches can be obtained with: - scythe -a adapter_file.fasta -o trimmed_sequences.fasta -m matches.txt sequences.fastq + scythe -a adapter_file.fasta -o trimmed_sequences.fastq -m matches.txt sequences.fastq By default, Illumina's quality scheme (pipeline > 1.3) is used. Sanger or Solexa (pipeline < 1.3) qualities can be specified with `-q`: - scythe -a adapter_file.fasta -q solexa -o trimmed_sequences.fasta sequences.fastq + scythe -a adapter_file.fasta -q solexa -o trimmed_sequences.fastq sequences.fastq Lastly, one can specify the minimum match length argument with `-n ` and the minimum length of sequence (discarded less than or equal to this parameter) to keep after trimming with `-M `: - scythe -a adapter_file.fasta -n 0 -M 10 -o trimmed_sequences.fasta sequences.fastq + scythe -a adapter_file.fasta -n 0 -M 10 -o trimmed_sequences.fastq sequences.fastq The default is 5. If this pre-processing is upstream of assembly on a very contaminated lane, decreasing this parameter could lead to *very* diff --git a/src/scythe.c b/src/scythe.c index a236a7c..5952a57 100644 --- a/src/scythe.c +++ b/src/scythe.c @@ -30,7 +30,7 @@ static const float default_prior = 0.3; #endif #ifndef VERSION -#define VERSION 0.993 +#define VERSION 0.994 #endif /* Options drawn from GNU's coreutils/src/system.h */