MarDRe Homepage

MarDRe v1.4 has been released and can be obtained from the Downloads section.

The main changes included in this version are:

MarDRe v1.3 has been released and can be obtained from the Downloads section.

The main changes included in this version are:

MarDRe now uses the Hadoop Sequence Parser (HSP) library to read input FASTQ/FASTA datasets. Overall performance is improved due to the custom sequence record readers provided by this library, especially in the paired-end mode when using a map-side join. Using HSP, this mode now executes a single MapReduce job (note that paired-end mode using a reduce-side join still needs to execute two MapReduce jobs)
Fix bug in paired-end mode scenarios

MarDRe v1.2 has been released and can be obtained from the Downloads section.

The main changes included in this version are:

Optimized paired-end mode using a map-side join (enabled by default)
Support for input/output datasets compressed with Gzip (.gz extension) and BZip2 (.bz2 extension) codecs. Read user's guide for more information
New command-line options (-q and -f) to specify the input file format for compressed datasets
The user can decide to compare only a certain number of bases for each read using a new command-line option (-c)
The number of reducers can now be specified using a new command-line option (-nr)
New configuration parameter to enable Snappy compression of the map output phase
New configuration parameter to specify HDFS block replication factor for output sequence files
New configuration parameter to specify the HDFS base path used by MarDRe to store both the output and intermediate files
Fix bug in paired-end mode when processing FASTA datasets

MarDRe v1.1 has been released and can be obtained from the Downloads section.

The main changes included in this version are:

Overall performance enhancements by reducing memory footprint, GC overhead and sequence parsing
Optimized paired-end mode
When two FASTQ reads are collapsed, now the one with the highest average quality is kept
The user can specify the output file names using new command-line options (-o and -r)
Sanity checks for the value of some configuration parameters
Minor bug fixes

MarDRe v1.0.1 has been released and can be obtained from the Downloads section.

The main changes included in this version are:

User's guide has been updated to specify that the current version of MarDRe does not take into account the quality scores for selecting the representative sequence when duplicated
Fix bug with the distribution tarball to include the parent directory

The first public release of MarDRe (v1.0) has been released and can be obtained from the Downloads section.