Mercurial > repos > nikhil-joshi > sickle
changeset 0:edb17624a6eb draft
Uploaded
| author | nikhil-joshi |
|---|---|
| date | Thu, 21 Jun 2012 20:43:16 -0400 |
| parents | |
| children | 7b37c85ba925 |
| files | sickle/LICENSE sickle/README.md sickle/sickle sickle/sickle.xml |
| diffstat | 4 files changed, 225 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sickle/LICENSE Thu Jun 21 20:43:16 2012 -0400 @@ -0,0 +1,19 @@ +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/sickle/README.md Thu Jun 21 20:43:16 2012 -0400 @@ -0,0 +1,107 @@ +# sickle - A windowed adaptive trimming tool for FASTQ files using quality + +## About + +Most modern sequencing technologies produce reads that have +deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases +in both regions negatively impact assembles, mapping, and downstream +bioinformatics analyses. + +Sickle is a tool that uses sliding windows along with quality and +length thresholds to determine when quality is sufficiently low to +trim the 3'-end of reads and also determines when the quality is +sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the +length threshold. It takes the quality values and slides a window +across them whose length is 0.1 times the length of the read. If this +length is less than 1, then the window is set to be equal to the +length of the read. Otherwise, the window slides along the quality +values until the average quality in the window rises above the threshold, at +which point the algorithm determines where within the window the rise occurs +and cuts the read and quality there for the 5'-end cut. Then when the average quality +in the window drops below the threshold, the algorithm determines where in the window +the drop occurs and cuts both the read and quality strings there for the 3'-end cut. +However, if the length of the remaining sequence is less than the minimum length threshold, +then the read is discarded entirely. 5'-end trimming can be disabled. + +Sickle also has an option to discard reads with any Ns in them. + +Sickle supports three types of quality values: Illumina, Solexa, +and Sanger. Note that the Solexa quality setting is an approximation +(the actual conversion is a non-linear transformation). The end +approximation is close. Illumina quality refers to qualities encoded +with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality +using CASAVA >= 1.8 is Sanger encoded. + +Note that Sickle will remove the 2nd fastq record header (on the "+" line) and replace it +with simply a "+". This is the default format for CASAVA >= 1.8. + +Sickle also supports gzipped file inputs. There is also a sickle.xml file +included in the package that can be used to add sickle to your local [Galaxy](http://galaxy.psu.edu/) server. + +## Requirements + +Sickle requires a C compiler; GCC or clang are recommended. Sickle +relies on Heng Li's kseq.h, which is bundled with the source. + +Sickle also requires Zlib, which can be obtained at +<http://www.zlib.net/>. + +## Building and Installing Sickle + +To build Sickle, enter: + + make + +Then, copy or move "sickle" to a directory in your $PATH. + +## Usage + +Sickle has two modes to work with both paired-end and single-end +reads: `sickle se` and `sickle pe`. + +Running sickle by itself will print the help: + + sickle + +Running sickle with either the "se" or "pe" commands will give help +specific to those commands: + + sickle se + sickle pe + +### Sickle Single End (`sickle se`) + +`sickle se` takes an input fastq file and outputs a trimmed version of +that file. It also has options to change the length and quality +thresholds for trimming, as well as disabling 5'-trimming and enabling removal +of sequences with Ns. + +#### Examples + + sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq + sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -q 33 -l 40 + sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -x -n + +### Sickle Paired End (`sickle pe`) + +`sickle pe` takes two paired-end files as input and outputs two +trimmed paired-end files as well as a "singles" file. The "singles" +file contains reads that passed filter in one of the paired-end files +but not the other. You can also change the length and quality +thresholds for trimming, as well as disable 5'-trimming and enable removal +of sequences with Ns. + +#### Examples + + sickle pe -f input_file1.fastq -r input_file2.fastq -t sanger \ + -o trimmed_output_file1.fastq -p trimmed_output_file2.fastq \ + -s trimmed_singles_file.fastq + + sickle pe -f input_file1.fastq -r input_file2.fastq -t sanger \ + -o trimmed_output_file1.fastq -p trimmed_output_file2.fastq \ + -s trimmed_singles_file.fastq -q 12 -l 15 + + sickle pe -f input_file1.fastq -r input_file2.fastq -t sanger \ + -o trimmed_output_file1.fastq -p trimmed_output_file2.fastq \ + -s trimmed_singles_file.fastq -n +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sickle/sickle.xml Thu Jun 21 20:43:16 2012 -0400 @@ -0,0 +1,99 @@ +<tool id="sickle" name="Sickle"> + <description>Windowed Adaptive Trimming of FastQ data</description> + + <command> + sickle $readtype.single_or_paired --quiet + + #if str($readtype.single_or_paired) == "se": + -f $input_single -t $qual_type -o $output_single + #end if + + #if str($readtype.single_or_paired) == "pe": + -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type + #end if + + #if str($qual_threshold) != "": + -q $qual_threshold + #end if + + #if str($length_threshold) != "": + -l $length_threshold + #end if + + #if $no_five_prime: + -x + #end if + + #if $discard_n: + -n + #end if + </command> + + <inputs> + <conditional name="readtype"> + <param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?"> + <option value="se" selected="true">Single-End</option> + <option value="pe">Paired-End</option> + </param> + + <when value="se"> + <param format="fastq, fastqsanger" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/> + </when> + + <when value="pe"> + <param format="fastq, fastqsanger" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/> + <param format="fastq, fastqsanger" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/> + </when> + </conditional> + + <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="qual_threshold" value="20" type="integer" optional="true" label="Quality Threshold"> + <validator type="in_range" min="0" message="Minimum value is 0"/> + </param> + + <param name="length_threshold" value="20" type="integer" optional="true" label="Length Threshold"> + <validator type="in_range" min="0" message="Minimum value is 0"/> + </param> + + <param name="no_five_prime" type="boolean" label="Don't do 5' trimming"/> + <param name="discard_n" type="boolean" label="Discard sequences with Ns"/> + </inputs> + + <outputs> + <data format="fastq" name="output_single" label="Single-End output of ${tool.name} on ${on_string}"> + <filter>(readtype['single_or_paired'] == 'se')</filter> + </data> + + <data format="fastq" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}"> + <filter>(readtype['single_or_paired'] == 'pe')</filter> + </data> + + <data format="fastq" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}"> + <filter>(readtype['single_or_paired'] == 'pe')</filter> + </data> + + <data format="fastq" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}"> + <filter>(readtype['single_or_paired'] == 'pe')</filter> + </data> + </outputs> + + <help> +Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses. + +Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5'-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely. 5'-end trimming can be disabled. + +Sickle also has an option to discard reads with any Ns in them. + +Sickle supports three types of quality values: Illumina, Solexa, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close. Illumina quality refers to qualities encoded with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality using CASAVA >= 1.8 is Sanger encoded. + +Note that Sickle will remove the 2nd fastq record header (on the "+" line) and replace it with simply a "+". This is the default format for CASAVA >= 1.8. + +Sickle also supports gzipped file inputs. + </help> + +</tool>