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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.  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
+