diff README.md @ 4:c70137414dcd draft

sickle v1.33

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+# 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 (or replaced with an "N" record). 5'-end 
+trimming can be disabled.
+
+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 and optional gzipped outputs. By default,
+Sickle will produce regular (i.e. not gzipped) output, regardless of the input.
+Sickle also has an option to truncate reads with Ns at the first N position.
+
+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.
+
+## Citation
+Sickle doesn't have a paper, but you can cite it like this:
+
+    Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files 
+    (Version 1.33) [Software].  Available at https://github.com/najoshi/sickle.
+
+## 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
+truncation 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 se -t sanger -g -f input_file.fastq -o trimmed_output_file.fastq.gz
+
+### Sickle Paired End (`sickle pe`)
+
+`sickle pe` can operate with two types of input.  First, it can take
+two paired-end files as input and outputs two trimmed paired-end files
+as well as a "singles" file.  The second form starts with a single
+combined input file of reads where you have already interleaved the
+reads from the sequencer.  In this form, you also supply a single
+output file name as well as a "singles" file.  The "singles" file
+contains reads that passed filter in either the forward or reverse
+direction, but not the other.  Finally, there is an option (-M) to only 
+produce one interleaved output file where any reads that did not pass 
+filter will be output as a FastQ record with a single "N" (whose quality 
+value is the lowest possible based upon the quality type), thus 
+preserving the paired nature of the data.  You can also change the length 
+and quality thresholds for trimming, as well as disable 5'-trimming and 
+enable truncation 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
+
+    sickle pe -c combo.fastq -t sanger -m combo_trimmed.fastq \
+    -s trimmed_singles_file.fastq -n
+
+    sickle pe -t sanger -g -f input_file1.fastq -r input_file2.fastq \
+    -o trimmed_output_file1.fastq.gz -p trimmed_output_file2.fastq.gz \
+    -s trimmed_singles_file.fastq.gz
+
+    sickle pe -c combo.fastq -t sanger -M combo_trimmed_all.fastq