changeset 2:6889442b27dc draft default tip

Uploaded
author aaronpetkau
date Sat, 04 Jul 2015 08:58:21 -0400
parents a444685f161c
children
files FLASH.sh FLASH.xml README tool_dependencies.xml
diffstat 4 files changed, 494 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FLASH.sh	Sat Jul 04 08:58:21 2015 -0400
@@ -0,0 +1,41 @@
+#/bin/bash
+
+#grab output files
+merged_reads=$1
+shift
+not_combined_1=$1
+shift
+not_combined_2=$1
+shift
+inter_not_combined=$1
+shift
+reads_and_pairs=$1
+shift
+log_file=$1
+shift
+
+flash $@ > $log_file
+sleep 5 #sleep because phil says so
+
+if [ -f out.notCombined_2.fastq ];
+then
+    mv out.notCombined_2.fastq $not_combined_2
+fi
+if [ -f out.notCombined_1.fastq ];
+then
+    mv out.notCombined_1.fastq $not_combined_1
+fi
+if [ -f out.notCombined.fastq ];
+then
+    mv out.notCombined.fastq $inter_not_combined
+fi
+if [ -f out.readsAndPairs.tab ];
+then
+    mv out.readsAndPairs.tab $reads_and_pairs
+fi
+if [ -f out.extendedFrags.fastq ];
+then
+    mv out.extendedFrags.fastq $merged_reads
+fi
+
+exit 0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FLASH.xml	Sat Jul 04 08:58:21 2015 -0400
@@ -0,0 +1,331 @@
+<tool id="FLASH" name="FLASH" version="1.3.0">
+  <description>merge paired-end reads from fragments that are shorter than twice the length of reads</description>
+  <command interpreter="bash">
+    FLASH.sh $extendedFrags $notCombined1 $notCombined2 $interNotCombined $readsAndPairs $log_file -o out -t 4 
+    #if $min_overlap
+      -m $min_overlap
+    #end if
+    #if $max_overlap
+      -M $max_overlap
+    #else
+      -M 250
+    #end if
+    #if $outputs.output_type == "Interleaved_fastq"
+      --interleaved-output
+	    #else if $outputs.output_type == "tab"
+      -To
+    #end if
+    #if $options.options_select == "advanced"
+      #if $options.max_mismatch_density
+	-x $options.max_mismatch_density
+      #end if
+      #if $options.phred_offset
+	-p $options.phred_offset
+      #end if
+      #if $options.read_length
+	-r $options.read_length
+      #end if
+      #if $options.fragment_length
+	-f $options.fragment_length
+      #end if
+      #if $options.fragment_stdev
+	-s $options.fragment_stdev
+      #end if
+      #if $options.cap_mismatch_quals
+	$options.cap_mismatch_quals
+      #end if
+      #if $options.quiet
+	$options.quiet
+      #end if
+    #end if 
+
+    #if $input_type.sPaired == "paired":
+       $input_type.pInput1 $input_type.pInput2
+    #elif $input_type.sPaired == "collections":
+       $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
+    #end if
+
+  </command>
+  <inputs>
+          <conditional name="input_type">
+            <param name="sPaired" type="select" label="Single Pair or Collection">
+              <option value="collections">Paired-end Collections</option>
+              <option value="paired">Paired-end</option>
+            </param>
+            <when value="paired">
+                <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
+                <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
+            </when>
+            <when value="collections">
+              <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
+            </when>
+          </conditional>
+
+	<param name="min_overlap" type="integer" label="Minimum overlap" optional="true"/>
+	<param name="max_overlap" type="integer" label="Maximum overlap" value="250" optional="true"/>
+	<conditional name="outputs">
+		<param name="output_type" type="select" label="Output type">
+                	<option value="Non-interleaved_fastq">Non-interleaved fastq</option>
+                	<option value="Interleaved_fastq">Interleaved fastq</option>
+                	<option value="tab">Tab-deliminated</option>
+	        </param>
+	</conditional>
+        <conditional name="options">
+		<param name="options_select" type="select" label="Options Type">
+			<option value="basic">Basic</option>
+			<option value="advanced">Advanced</option>
+		</param>
+		<when value="advanced">
+			<param name="max_mismatch_density" type="float" label="Maximum mismatch density" optional="true"/>
+			<param name="phred_offset" type="select" label="Phred-offset" optional="true">
+				<option value="33">33</option>
+				<option value="64">64</option>
+			</param>
+			<param name="read_length" type="integer" label="Average read length" optional="true"/>
+			<param name="fragment_length" type="integer" label="Fragment length" optional="true"/>
+			<param name="fragment_stdev" type="integer" label="Fragment length standard deviation" optional="true"/>
+			<param name="cap_mismatch_quals" type="boolean" label="Cap mismatch quality scores" truevalue="--cap-mismatch-quals" optional="true"/>
+			<!--<param name="compress" type="boolean" label="Compress output files with gzip" optional="true"/>
+			<param name="compress_prog" type="text" label="Compression program" optional="true"/>
+			<param name="compress_prog_args" type="text" label="Compression program arguments" optional="true"/> <~~~~~~~~Phil says the compression options aren't needed-->
+			<param name="quiet" type="boolean" label="Do not print informational messages" truevalue="-q" optional="true"/>
+		</when>
+        </conditional>
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="extendedFrags" label="Merged reads">
+	<filter>outputs['output_type'] != "tab"</filter>
+    </data>
+    <data format="fastqsanger" name="notCombined1" label="Read 1 of mate pairs not merged">
+	<filter>outputs['output_type'] == "Non-interleaved_fastq"</filter>
+    </data>
+    <data format="fastqsanger" name="notCombined2" label="Read 2 of mate pairs not merged">
+	<filter>outputs['output_type'] == "Non-interleaved_fastq"</filter>
+    </data>
+    <data format="fastqsanger" name="interNotCombined" label="Interleaved non-combined pairs">
+	<filter>outputs['output_type'] == "Interleaved_fastq"</filter>
+    </data>
+    <data format="tabular" name="readsAndPairs" label="Merged and non-merged pairs">
+	<filter>outputs['output_type'] == "tab"</filter>
+    </data>
+    <data format="txt" name="log_file" label="Log file"/>
+   <!-- <data format="txt" name="numericHistogram" label="Numeric histogram of merged read lengths"/>
+    <data format="txt" name="visualHistogram" label="Visual histogram of merged read lengths"/>-->
+  </outputs>
+  <requirements>
+    <requirement type="package" version="1.2.9">FLASH</requirement>
+  </requirements>
+  <help>
+----------------------------------------------------------------------------
+                                 DESCRIPTION                                
+----------------------------------------------------------------------------
+
+FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool
+to merge paired-end reads that were generated from DNA fragments whose
+lengths are shorter than twice the length of reads.  Merged read pairs result
+in unpaired longer reads, which are generally more desired in genome
+assembly and genome analysis processes.
+
+Briefly, the FLASH algorithm considers all possible overlaps at or above a
+minimum length between the reads in a pair and chooses the overlap that
+results in the lowest mismatch density (proportion of mismatched bases in
+the overlapped region).  Ties between multiple overlaps are broken by
+considering quality scores at mismatch sites.  When building the merged
+sequence, FLASH computes a consensus sequence in the overlapped region.
+More details can be found in the original publication
+(http://bioinformatics.oxfordjournals.org/content/27/21/2957.full).
+
+Limitations of FLASH include:
+   - FLASH cannot merge paired-end reads that do not overlap.
+   - FLASH cannot merge read pairs that have an outward orientation, either
+     due to being "jumping" reads or due to excessive trimming.
+   - FLASH is not designed for data that has a significant amount of indel
+     errors (such as Sanger sequencing data).  It is best suited for Illumina
+     data.
+
+----------------------------------------------------------------------------
+                               MANDATORY INPUT
+----------------------------------------------------------------------------
+
+The most common input to FLASH is two FASTQ files containing read 1 and read 2
+of each mate pair, respectively, in the same order.
+
+Alternatively, you may provide one FASTQ file, which may be standard input,
+containing paired-end reads in either interleaved FASTQ (see the
+--interleaved-input option) or tab-delimited (see the --tab-delimited-input
+option) format.  In all cases, gzip compressed input is autodetected.  Also,
+in all cases, the PHRED offset is, by default, assumed to be 33; use the
+--phred-offset option to change it.
+
+----------------------------------------------------------------------------
+                                   OUTPUT
+----------------------------------------------------------------------------
+
+The default output of FLASH consists of the following files:
+
+   - out.extendedFrags.fastq      The merged reads.
+   - out.notCombined_1.fastq      Read 1 of mate pairs that were not merged.
+   - out.notCombined_2.fastq      Read 2 of mate pairs that were not merged.
+   - out.hist                     Numeric histogram of merged read lengths.
+   - out.histogram                Visual histogram of merged read lengths.
+
+FLASH also logs informational messages to standard output.  These can be
+redirected to a file, as in the following example:
+
+  $ flash reads_1.fq reads_2.fq | tee flash.log
+
+In addition, FLASH supports several features affecting the output:
+
+   - Writing the merged reads directly to standard output (--to-stdout)
+   - Writing gzip compressed output files (-z) or using an external
+     compression program (--compress-prog)
+   - Writing the uncombined read pairs in interleaved FASTQ format
+     (--interleaved-output)
+   - Writing all output reads to a single file in tab-delimited format
+     (--tab-delimited-output)
+
+----------------------------------------------------------------------------
+                                   OPTIONS
+----------------------------------------------------------------------------
+
+  -m, --min-overlap=NUM   The minimum required overlap length between two
+                          reads to provide a confident overlap.  Default:
+                          10bp.
+
+  -M, --max-overlap=NUM   Maximum overlap length expected in approximately
+                          90% of read pairs.  It is by default set to 70bp,
+                          which works well for 100bp reads generated from a
+                          180bp library, assuming a normal distribution of
+                          fragment lengths.  Overlaps longer than the maximum
+                          overlap parameter are still considered as good
+                          overlaps, but the mismatch density (explained below)
+                          is calculated over the first max_overlap bases in
+                          the overlapped region rather than the entire
+                          overlap.  Default: 70bp, or calculated from the
+                          specified read length, fragment length, and fragment
+                          length standard deviation.
+
+  -x, --max-mismatch-density=NUM
+                          Maximum allowed ratio between the number of
+                          mismatched base pairs and the overlap length.
+                          Two reads will not be combined with a given overlap
+                          if that overlap results in a mismatched base density
+                          higher than this value.  Note: Any occurence of an
+                          'N' in either read is ignored and not counted
+                          towards the mismatches or overlap length.  Our
+                          experimental results suggest that higher values of
+                          the maximum mismatch density yield larger
+                          numbers of correctly merged read pairs but at
+                          the expense of higher numbers of incorrectly
+                          merged read pairs.  Default: 0.25.
+
+  -p, --phred-offset=OFFSET
+                          The smallest ASCII value of the characters used to
+                          represent quality values of bases in FASTQ files.
+                          It should be set to either 33, which corresponds
+                          to the later Illumina platforms and Sanger
+                          platforms, or 64, which corresponds to the
+                          earlier Illumina platforms.  Default: 33.
+
+  -r, --read-len=LEN
+
+  -f, --fragment-len=LEN
+
+  -s, --fragment-len-stddev=LEN
+                          Average read length, fragment length, and fragment
+                          standard deviation.  These are convenience parameters
+                          only, as they are only used for calculating the
+                          maximum overlap (--max-overlap) parameter.
+                          The maximum overlap is calculated as the overlap of
+                          average-length reads from an average-size fragment
+                          plus 2.5 times the fragment length standard
+                          deviation.  The default values are -r 100, -f 180,
+                          and -s 18, so this works out to a maximum overlap of
+                          65 bp.  If --max-overlap is specified, then the
+                          specified value overrides the calculated value.
+
+                          If you do not know the standard deviation of the
+                          fragment library, you can probably assume that the
+                          standard deviation is 10% of the average fragment
+                          length.
+
+  --cap-mismatch-quals    Cap quality scores assigned at mismatch locations
+                          to 2.  This was the default behavior in FLASH v1.2.7
+                          and earlier.  Later versions will instead calculate
+                          such scores as the
+                          absolute value of the difference in quality scores,
+                          but at least 2.  Essentially, the new behavior
+                          prevents a low quality base call that is likely a
+                          sequencing error from significantly bringing down
+                          the quality of a high quality, likely correct base
+                          call.
+
+  --interleaved-input     Instead of requiring files MATES_1.FASTQ and
+                          MATES_2.FASTQ, allow a single file MATES.FASTQ that
+                          has the paired-end reads interleaved.  Specify "-"
+                          to read from standard input.
+
+  --interleaved-output    Write the uncombined pairs in interleaved FASTQ
+                          format.
+
+  -I, --interleaved       Equivalent to specifying both --interleaved-input
+                          and --interleaved-output.
+
+  -Ti, --tab-delimited-input
+                          Assume the input is in tab-delimited format
+                          rather than FASTQ, in the format described below in
+                          '--tab-delimited-output'.  In this mode you should
+                          provide a single input file, each line of which must
+                          contain either a read pair (5 fields) or a single
+                          read (3 fields).  FLASH will try to combine the read
+                          pairs.  Single reads will be written to the output
+                          file as-is if also using --tab-delimited-output;
+                          otherwise they will be ignored.  Note that you may
+                          specify "-" as the input file to read the
+                          tab-delimited data from standard input.
+
+  -To, --tab-delimited-output
+                          Write output in tab-delimited format (not FASTQ).
+                          Each line will contain either a combined pair in the
+                          format 'tag &lt;tab&gt; seq &lt;tab&gt; qual' or an uncombined
+                          pair in the format 'tag &lt;tab&gt; seq_1 &lt;tab&gt; qual_1
+                          &lt;tab&gt; seq_2 &lt;tab&gt; qual_2'.
+
+  -o, --output-prefix=PREFIX
+                          Prefix of output files.  Default: "out".
+
+  -d, --output-directory=DIR
+                          Path to directory for output files.  Default:
+                          current working directory.
+
+  -c, --to-stdout         
+			  Write the combined reads to standard output.  In
+                          this mode, with FASTQ output (the default) the
+                          uncombined reads are discarded.  With tab-delimited
+                          output, uncombined reads are included in the
+                          tab-delimited data written to standard output.
+                          In both cases, histogram files are not written,
+                          and informational messages are sent to standard
+                          error rather than to standard output.
+
+  --suffix=SUFFIX, --output-suffix=SUFFIX
+                          Use SUFFIX as the suffix of the output files
+                          after ".fastq".  A dot before the suffix is assumed,
+                          unless an empty suffix is provided.  Default:
+                          nothing; or 'gz' if -z is specified; or PROG if
+                          --compress-prog=PROG is specified.
+
+  -t, --threads=NTHREADS  Set the number of worker threads.  This is in
+                          addition to the I/O threads.  Default: number of
+                          processors.  Note: if you need FLASH's output to
+                          appear deterministically or in the same order as
+                          the original reads, you must specify -t 1
+                          (--threads=1).
+
+  -q, --quiet             Do not print informational messages.
+
+  -h, --help              Display this help and exit.
+
+  -v, --version           Display version.
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Sat Jul 04 08:58:21 2015 -0400
@@ -0,0 +1,106 @@
+Tool wrapper by Brian Yeo
+brian.yeo@phac.aspc.gc.ca
+
+                                  INTRODUCTION
+
+FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool
+to merge paired-end reads that were generated from DNA fragments whose
+lengths are shorter than twice the length of reads.  Merged read pairs result
+in unpaired longer reads, which are generally more desired in genome
+assembly and genome analysis processes.
+
+Briefly, the FLASH algorithm considers all possible overlaps at or above a
+minimum length between the reads in a pair and chooses the overlap that
+results in the lowest mismatch density (proportion of mismatched bases in
+the overlapped region).  Ties between multiple overlaps are broken by
+considering quality scores at mismatch sites.  When building the merged
+sequence, FLASH computes a consensus sequence in the overlapped region.
+More details can be found in the original publication
+(http://bioinformatics.oxfordjournals.org/content/27/21/2957.full).
+
+Limitations of FLASH include:
+   - FLASH cannot merge paired-end reads that do not overlap.
+   - FLASH cannot merge read pairs that have an outward orientation, either
+     due to being "jumping" reads or due to excessive trimming.
+   - FLASH is not designed for data that has a significant amount of indel
+     errors (such as Sanger sequencing data).  It is best suited for Illumina
+     data.
+
+                                  INSTALLATION
+
+On UNIX-compatible systems, including GNU/Linux and Mac OS X, you must compile
+FLASH from source.  The only dependency, other than functions that are expected
+to be available in the C library, is the zlib data compression library.  To
+install FLASH, download the tarball, untar it, and compile the code using the
+provided Makefile:
+
+    $ tar xzf FLASH-1.2.9.tar.gz
+    $ cd FLASH-1.2.9
+    $ make
+
+The executable file that is produced is named 'flash'.  To run it from the
+command line you must copy it to a location on your $PATH variable, or else run
+it with a path including a directory, such as "./flash".
+
+FLASH also runs on Windows, and you can compile it on Windows using MinGW.
+However, for convenience you may instead download a standalone Windows binary
+from the SourceForge page (https://sourceforge.net/projects/flashpage/).
+
+                                     USAGE
+
+Please compile FLASH and run `flash --help' to see command-line usage
+information and information about input/output files.
+
+                                 MULTITHREADING
+
+By default, FLASH uses multiple threads.  There are "combiner" threads that do
+the actual read combining, as well as up to 5 threads that are used for I/O (up
+to 2 readers, up to 3 writers).  The default number of combiner threads is the
+number of processors; however, it can be adjusted with the -t  option (long
+option: --threads).
+
+When multiple combiner threads are used, the order of the combined and
+uncombined reads in the output files will be nondeterministic.  If you need to
+enforce that the output reads appear in the same order as the input, you must
+specify --threads=1.
+
+                                  PERFORMANCE
+
+Since the FLASH algorithm considers each read pair independently, FLASH will, by
+default, process read pairs in parallel.  FLASH v1.2.9 and later also make use
+of vector instructions available on modern x86 CPUs.  Consequently, FLASH works
+quite fast, even with low-cost computing resources.  As an example, we ran FLASH
+v1.2.9 on a laptop with a dual-core 2.3 GHz AMD x86_64 processor and it
+processed one million 101-bp read pairs in 11.6 seconds with the default
+parameters.  Less than 2 MB of memory was used.  Actual timing results will
+vary, but they will depend primarily on the number of CPUs available, the speed
+of each CPU, and on the I/O speed of reading the input files and writing the
+output files.  FLASH is designed to be scalable to dozens of processors,
+although its speed may be limited by I/O in such cases.
+
+                                   ACCURACY
+
+With reads' error rate of 1% or less, FLASH processes over 99% of read pairs
+correctly.  With error rate of 2%, FLASH processes over 98% of read pairs
+correctly when default parameters are used. With more aggressive parameters
+(i.e., -x 0.35), FLASH processes over 90% of read pairs correctly even when the
+error rate is 5%.
+
+                                  PUBLICATION
+
+Title:   FLASH: fast length adjustment of short reads to improve genome assemblies
+Authors: Tanja Mago─Ź and Steven L. Salzberg
+URL:     http://bioinformatics.oxfordjournals.org/content/27/21/2957.full
+
+                                    LICENSE
+
+FLASH is released under the GNU General Public License Version 3 or later (see
+COPYING).
+
+                          COMMENTS/QUESTIONS/REQUESTS
+
+Send an e-mail to flash.comment@gmail.com
+
+Other versions are available from the SourceForge page:
+
+https://sourceforge.net/projects/flashpage/
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Jul 04 08:58:21 2015 -0400
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tool_dependency>
+        <package name="FLASH" version="1.2.9">
+                <install version="1.0">
+                        <actions>
+                                <action type="download_by_url" target_filename="FLASH-1.2.9.tar.gz">http://sourceforge.net/projects/flashpage/files/FLASH-1.2.9.tar.gz/download</action>
+				<action type="shell_command">make</action>
+                                <action type="shell_command">cp -r * $INSTALL_DIR</action>
+                                <action type="chmod"><file mode="777">$INSTALL_DIR/flash</file></action>
+                                <action type="set_environment">
+                                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                                </action>
+                        </actions>
+                </install>
+        </package>
+</tool_dependency>