HTStream

 

 

HTStream is a suite of preprocessing applications for high throughput sequencing data (ex. Illumina). A Fast C++ implementation, designed with discreet functionality that can be pipelined together using standard unix piping.

Example:

hts_Stats -L sample1.json -N "initial Stats" \
    -1 sample1_S1_L001_R1_001.fastq.gz \  
    -2 sample1_S1_L001_R1_001.fastq.gz | \  
hts_AdapterTrimmer -A sample1.json -N "trim adapters" | \  
hts_LengthFilter -A sample1.json -N "remove reads < 50bp" \  
    -m 50 | \  
hts_Stats -A sample1.json -N "final Stats" \  
    -f sample1_preprocessed  

Quick Installation

Install binaries for linux systems:

On Linux systems, the easiest and most straight forward option is to download and unpack the pre-compiled binaries to somewhere on your $PATH.

wget https://github.com/ibest/HTStream/releases/download/v1.2.0-release/HTStream_v1.2.0-release.tar.gz

tar xvf HTStream_v1.2.0-release.tar.gz

Install from Bioconda:

HTStream is available through the Bioconda channel. Visit Miniconda.

conda install -c bioconda htstream

If you wish to install from source or the development version, see our more [complete installation]({{ site.baseurl }}/install) instructions.

Application Descriptions

HTStream includes the following applications:

[hts_AdapterTrimmer]({{ site.baseurl }}/applications/hts_AdapterTrimmer): Identify and remove adapter sequences.
[hts_CutTrim]({{ site.baseurl }}/applications/hts_CutTrim): Discreet 5' and/or 3' basepair trimming.
[hts_LengthFilter]({{ site.baseurl }}/applications/hts_LengthFilter): Remove reads outside of min and/or max length.
[hts_NTrimmer]({{ site.baseurl }}/applications/hts_NTrimmer): Extract the longest subsequence with no Ns.
[hts_Overlapper]({{ site.baseurl }}/applications/hts_Overlapper): Overlap paired end reads, removing adapters when present.
[hts_PolyATTrim]({{ site.baseurl }}/applications/hts_PolyATTrim): Identify and remove polyA/T sequence.
[hts_Primers]({{ site.baseurl }}/applications/hts_Primers) - Identify and optionally remove 5' and/or 3' primer sequence.
[hts_QWindowTrim]({{ site.baseurl }}/applications/hts_QWindowTrim) - 5' and/or 3' quality score base trimming using windows.
[hts_SeqScreener]({{ site.baseurl }}/applications/hts_SeqScreener): Identify and remove/keep/count contaminants (default phiX).
[hts_Stats]({{ site.baseurl }}/applications/hts_Stats) - Compute read stats.
[hts_SuperDeduper]({{ site.baseurl }}/applications/hts_SuperDeduper): Identify and remove PCR duplicates.

We hope in the long run to include any and all needed preprocessing routines.

A [detailed description]({{ site.baseurl }}/applications) of the project.

Example Workflows

You can build your own preprocessing pipeline specific to the experiment and sequencing library, but we've put together a few [example pipelines]({{ site.baseurl }}/workflows) for you.

Contributing

First please read code of conduct.

If you encounter any bugs or have suggestions for improvement, please post them to issues.

We'd love to accept code and/or application additions! If your interested in contributing please read our contributing guidelines.

Thanks for using HTStream!