--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scythe/LICENSE	Thu Jun 21 20:54:58 2012 -0400
@@ -0,0 +1,20 @@
+MIT License
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use, copy,
+modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scythe/README.md	Thu Jun 21 20:54:58 2012 -0400
@@ -0,0 +1,191 @@
+# Scythe - A very simple adapter trimmer (version 0.981 BETA)
+
+Scythe and all supporting documentation 
+Copyright (c) Vince Buffalo, 2011-2012
+
+Contact: Vince Buffalo <vsbuffaloAAAAA@gmail.com> (with the poly-A tail removed)
+
+If you wish to report a bug, please open an issue on Github
+(http://github.com/vsbuffalo/scythe/issues) so that it can be
+tracked. You can contact me as well, but please open an issue first.
+
+## About
+
+Scythe uses a Naive Bayesian approach to classify contaminant
+substrings in sequence reads. It considers quality information, which
+can make it robust in picking out 3'-end adapters, which often include
+poor quality bases.
+
+Most next generation sequencing reads have deteriorating quality
+towards the 3'-end. It's common for a quality-based trimmer to be
+employed before mapping, assemblies, and analysis to remove these poor
+quality bases. However, quality-based trimming could remove bases that
+are helpful in identifying (and removing) 3'-end adapter
+contaminants. Thus, it is recommended you run Scythe *before*
+quality-based trimming, as part of a read quality control pipeline.
+
+The Bayesian approach Scythe uses compares two likelihood models: the
+probability of seeing the matches in a sequence given contamination,
+and not given contamination. Given that the read is contaminated, the
+probability of seeing a certain number of matches and mistmatches is a
+function of the quality of the sequence. Given the read is not
+contaminated (and is thus assumed to be random sequence), the
+probability of seeing a certain number of matches and mismatches is
+chance. The posterior is calculated across both these likelihood
+models, and the class (contaminated or not contaminated) with the
+maximum posterior probability is the class selected.
+
+## Requirements
+
+Scythe can be compiled using GCC or Clang; compilation during
+development used the latter. Scythe relies on Heng Li's kseq.h, which
+is bundled with the source.
+
+Scythe requires Zlib, which can be obtained at <http://www.zlib.net/>.
+
+## Building and Installing Scythe
+
+To build Scythe, enter:
+
+    make build
+
+Then, copy or move "scythe" to a directory in your $PATH.
+
+## Usage
+
+Scythe can be run minimally with:
+
+    scythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq
+
+By default, the prior contamination rate is 0.05. This can be changed
+(and one is encouraged to do so!) with:
+
+    scythe -a adapter_file.fasta -p 0.1 -o trimmed_sequences.fastq sequences.fastq
+
+If you'd like to use standard out, it is recommended you use the
+--quiet option:
+
+    scythe -a adapter_file.fasta --quiet sequences.fastq > trimmed_sequences.fastq
+
+Also, more detailed output about matches can be obtained with:
+
+    scythe -a adapter_file.fasta -o trimmed_sequences.fasta -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
+
+Lastly, a minimum match length argument can be specified with -n <integer>:
+
+    scythe -a adapter_file.fasta -n 0 -o trimmed_sequences.fasta 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*
+liberal trimming, i.e. of only a few bases. 
+
+## Notes
+
+Scythe only checks for 3'-end contaminants, up to the adapter's length
+into the 3'-end. For reads with contamination in *any* position, the
+program TagDust (<http://genome.gsc.riken.jp/osc/english/dataresource/>)
+is recommended. Scythe has the advantages of allowing fuzzier matching
+and being base quality-aware, while TagDust has the advantages of very
+fast matching (but allowing few mismatches, and not considering
+quality) and FDR. TagDust also removes contaminated reads *entirely*, while
+Scythe trims off contaminants. 
+
+A possible pipeline would run FASTQ reads through Scythe, then
+TagDust, then a quality-based trimmer, and finally through a read
+quality statistics program such as qrqc
+(<http://bioconductor.org/packages/devel/bioc/html/qrqc.html>) or FASTqc
+(<http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/>).
+
+## FAQ 
+
+### Does Scythe work with paired-end data?
+
+Scythe does work with paired-end data. Each file must be run
+separately, but Scythe will not remove reads entirely leaving
+mismatched pairs.
+
+In some cases, barcodes are ligated to both the 3'-end and 5'-end of
+reads. 5'-end removal is trivial since base calling is near-perfect
+there, but 3'-end removal can be trickier. Some users have created
+Scythe adapter files that contain all possible barcodes concatenated
+with possible adapters, so that both can be recognized and
+removed. This has worked well and is recommended for cases when 3'-end
+quality deteriorates and prevents barcode removal. Newer Illumina
+chemistry has the barcode separated from the fragment, so that it
+appears as an entirely separate read and is used to demultiplex sample
+reads by Illumina's CASAVA pipeline.
+
+### Does Scythe work on 5'-end or other contaminants?
+
+No. Embracing the Unix tool philosophy that tools should do one thing
+very well, Scythe just removes 3'-end contaminants where there could
+be multiple base mismatches due to poor base quality. N-mismatch
+algorithms (such as TagDust) don't consider base qualities. Scythe
+will allow more mismatches in an alignment if the mismatched bases are
+of low quality.
+
+**Scythe only checks as far in as the entire adapter contaminant's
+length.** However, some investigation has shown that Illumina
+pipelines sometimes produce reads longer than the read length +
+adapter length. The extra bases have always been observed to be
+A's. Some testing has shown this can be addressed by appending A's to
+the adapters in the adapters file. Since Scythe begins by checking for
+contamination from the 5'-end of the adapter, this won't affect the
+normal adapter contaminant cases.
+
+### What does the numeric output from Scythe mean?
+
+For each adapter in the file, the contaminants removed by position are
+returned via standard error. For example:
+
+    Adapter 1 'fake adapter' contamination occurences:
+    [10, 2, 4, 5, 6]
+
+indicates that "fake adapter" is 5 bases long (the length of the array
+returned), and that there were 10 contaminants found of first base (-n
+was set to 0 then), 2 of the first two bases, 4 contaminants of the
+first 3 bases, 5 of the first 4 bases, etc.
+
+### Does Scythe work on FASTA files?
+
+No, as these have no quality information.
+
+### How can I report a bug? 
+
+See the section below.
+
+### How does Scythe compare to program "x"?
+
+As far as I know, Scythe is the only program that employs a Bayesian
+model that allows prior contaminant estimates to be used. This prior
+is a more realistic approach than setting a fixed number of mismatches
+because we can visually estimate it with the Unix tool `less`.
+
+Scythe also looks at base-level qualities, *not* just a fixed level of
+mismatches. A fixed number of mismatches is a bad approach with data
+our group (the UC Davis Bioinformatics Core) has seen, as a small bad
+quality run can quickly exhaust even a high numbers of fixed
+mismatches and lead to higher false negatives.
+
+## Reporting Bugs
+
+Scythe is free software and is proved without a warranty. However, I
+am proud of this software and I will do my best to provide updates,
+bug fixes, and additional documentation as needed. Please report all
+bugs and issues to Github's issue tracker
+(http://github.com/vsbuffalo/scythe/issues). If you want to email me,
+do so in addition to an issue request.
+
+If you have a suggestion or comment on Scythe's methods, you can email
+me directly.
+
+## Is there a paper about Scythe?
+
+I am currently writing a paper on Scythe's methods. In my preliminary
+testing, Scythe has fewew false positives and false negatives than
+it competitors.
\ No newline at end of file

Binary file scythe/scythe has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scythe/scythe.xml	Thu Jun 21 20:54:58 2012 -0400
@@ -0,0 +1,66 @@
+<tool id="scythe" name="Scythe">
+	<description>Trimming adapters/contaminants using a Naive Bayesian classifier</description>
+
+	<command>
+		scythe --quiet -a $adapter_file -q $qual_type
+
+		#if str($add_tag) == "add_tag_true":
+		-t
+		#end if
+
+		#if str($prior) != "":
+		-p $prior
+		#end if
+
+		#if str($min_match) != "":
+		-n $min_match
+		#end if
+
+		#if str($matches_file) == "matches_file_true":
+		-m $output_matches
+		#end if
+
+		-o $output_trimmed $input_fastq 2> /dev/null
+	</command>
+
+	<inputs>
+		<param format="fastq, fastqsanger" name="input_fastq" type="data" optional="false" label="FastQ Reads"/>
+
+		<param format="fasta" name="adapter_file" type="data" optional="false" label="Adapter/Contaminant file (in fasta format)"/>
+
+		<param name="qual_type" type="select" optional="false" label="Quality type">
+			<option value="illumina" selected="true">Illumina</option>
+			<option value="solexa">Solexa</option>
+			<option value="sanger">Sanger</option>
+		</param>
+
+		<param name="add_tag" type="boolean" checked="false" truevalue="add_tag_true" falsevalue="add_tag_false" label="Add a tag to the header indicating that Scythe cut a sequence?"/>
+
+		<param name="matches_file" type="boolean" checked="false" truevalue="matches_file_true" falsevalue="matches_file_false" label="Also output another file with details about adapter/contaminant matches?"/>
+
+		<param name="prior" value="0.05" type="float" optional="true" label="Prior" help="The prior contamination rate">
+			<validator type="in_range" min="0" message="Minimum value is 0"/>
+		</param>
+
+		<param name="min_match" value="0" type="integer" optional="true" label="Smallest length adapter/contaminant to consider">
+			<validator type="in_range" min="0" message="Minimum value is 0"/>
+		</param>
+	</inputs>
+
+	<outputs>
+		<data format_source="input_fastq" name="output_trimmed" label="Adapter/Contaminant Trimmed FastQ using ${tool.name} on ${on_string}"/>
+
+		<data format="txt" name="output_matches" label="Matches of Adapters/Contaminants using ${tool.name} on ${on_string}">
+		<filter>(matches_file == True)</filter>
+		</data>
+	</outputs>
+
+	<help>
+Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases.
+
+Most next generation sequencing reads have deteriorating quality towards the 3'-end. It's common for a quality-based trimmer to be employed before mapping, assemblies, and analysis to remove these poor quality bases. However, quality-based trimming could remove bases that are helpful in identifying (and removing) 3'-end adapter contaminants. Thus, it is recommended you run Scythe before quality-based trimming, as part of a read quality control pipeline.
+
+The Bayesian approach Scythe uses compares two likelihood models: the probability of seeing the matches in a sequence given contamination, and not given contamination. Given that the read is contaminated, the probability of seeing a certain number of matches and mistmatches is a function of the quality of the sequence. Given the read is not contaminated (and is thus assumed to be random sequence), the probability of seeing a certain number of matches and mismatches is chance. The posterior is calculated across both these likelihood models, and the class (contaminated or not contaminated) with the maximum posterior probability is the class selected.
+	</help>
+
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scythe/solexa_adapters.JNF.fa	Thu Jun 21 20:54:58 2012 -0400
@@ -0,0 +1,4 @@
+>Solexa 3' adapter 1
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAA
+>Solexa 3' adapter 2
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAA