hmusket

K-mer spectrum corrector based on Hadoop

Requisites

• Java Develpment Environment (JDK) version 1.6 or above
• Make sure you have a working Apache Maven distribution version 3 or above
• A version of hsp (Hadoop Sequence Parser) in your Maven repository
  • Do you need help? Check this out
• Hadoop 2.8.0 or above
• g++ (development version: 6.3.0)
• GNU Make (development version: 4.1)
• Upgrade Commons-cli version (1.2 --> 1.4) in hadoop/share/hadoop/common (TODO: improve this)

Authors

• Luis Lorenzo Mosquera (https://github.com/luislorenzom)
• Roberto R. Éxposito (http://gac.udc.es/~rreye)
• Jorge González Domínguez (http://gac.udc.es/~jgonzalezd)

Do you want to compile hmusket from scrath?

• Clone this project
• Generate the header file for java side call (resource/make.sh)
• Configure in src/main/native/MakeFile.common where is musket source files.
  • Don't you have a musket source code copy? Download it
• Also in src/main/native execute make to compile musket and create the shared library
• Once you have the shared library created copy it from lib folder (root folder) and paste it in $HADOOP_HOME/lib/native
• Additionally you have to change your common-cli library in your hadoop cluster
  • Copy the commons-cli-1.4 (from .m2/) to $HADOOP_HOME/share/hadoop/common/lib
• Finally compile with Maven hmusket mvn clean package

How to run hmusket?

Flags cheat sheet

usage: hmusket -fileIn -fileOut -fileType <a/q> [-inorder] [-k <int/unit>] [-lowercase] [-maxbuff ] [-maxerr ] [-maxiter ] [-maxtrim ] [-minmulti ] [-multik ] [-o ] [-omulti ] [-p ] [-zlib ]

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-fileIn <filePath>         File where there are the sequences

-fileOut <filePath>      File where there want to save the output

-fileType <a/q>            File type for FASTA files and for FASTQ files

-k <int/unit>                  Specify two paramters: k-mer size and estimated total number of k-mers for this k-mer size)

-lowercase                    Write corrected bases in lowercase, default=0

-maxbuff <int>            Capacity of message buffer for each worker, default=1024

-maxerr <int>              Maximal number of mutations in any region of length#k, default=4

-maxiter <int>             Maximal number of correcting iterations per k-mer size, default=2

-maxtrim <int>           Maximal number of bases that can be trimmed, default=0

-minmulti <int>          Minimum multiplicty for correct k-mers [only applicable when not using multiple k-mer sizes],default=0

-multik <bool>             Enable the use of multiple k-mer sizes, default=0

-o <str>                            The single output file name

-omulti <str>                 Prefix of output file names, one input corresponding one output

-p <int>                            Number of threads [>=2], default=2

-zlib <int>                       Zlib-compressed output, default=0

Some runs examples

# Single-end dataset
user@host:~$ hadoop jar Hmusket-1.0.jar es.udc.gac.hmusket.HMusket -fileIn ~/datasets/single-end.fastq -fileOut output1 -fileType q

# Pair-end dataset
user@host:~$ hadoop jar Hmusket-1.0.jar es.udc.gac.hmusket.HMusket -fileIn  ~/datasets/pair-end_1.fasta ~/datasets/pair-end_2.fasta -fileOut output2 -fileType a -p 4

License

This software is distributed as free software and is publicity available under the GPLv3 license (see the LICENSE file for more details)