
Release Notes for SHORE version 0.7
===================================

v0.7.1
------

 - import: additional demultiplex option '-w 2ndread'
 - improved read/write error reporting
 - fixed a potential problem with bwa

v0.7.0
------
 
News:
 - many fixes to the 'qVar' tool
 - import: allow trimming both ends of reads
 - import: support the 2nd/3rd read barcoding protocol
 - fixed BLAT and ELAND aligners
 - all options may be configured via configuration files in ~/.config/shore

Release Notes for SHORE version 0.6
===================================

v0.6.2
------

Fixes for important bugs in v0.6.1:

 - correct4pe: don't crash if there is no 'single' directory
 - fix the --peflags alignment filter

v0.6.1
------

Fixes for important bugs in v0.6.0:

 - alignment using bowtie (mapflowcell)
 - fastq file reading (convert, mapflowcell)
 - setting temporary directory using 'shore -T' (correct4pe)

v0.6.0
------

New features:
 - New improved SNP, indel and CNV caller SHORE 'qVar' replacing SHORE 'consensus'
 - Alignment quick-viewer SHORE 'mapdisp'
 - Gzip compatible indexed file compression SHORE 'compress'
 - Alignment file indexing SHORE '2dex' for fast retrieval of alignments from
   specific regions of the genome

Improvements:
 - Improved converter with e.g. improved SAM/BAM support
 - New file compression supported in most tools
 - Distributed memory parallelization for 'mapflowcell'
 - All information filtered by SHORE 'import' can be fully recovered
 ... and many more.


Release Notes for SHORE version 0.5
===================================

SHORE source code and binaries are now available under GPL at
https://sourceforge.net/projects/shore/

New features:
1) SOLiD support inlcuding most analyses available for Illumina
2) Structural variant detection: SHORE 'structure'
2) ChIP-seq analysis using SHORE 'peak'
3) Expression analysis: SHORE 'coverage', 'count'
4) Small RNA analysis: SHORE 'sRNA'
5) RNA editing analysis: SHORE 'RNAediting'
6) Statistics: SHORE 'binom_test', 'mtc', 'ranksim'
7) Annotation: SHORE 'annotate'
8) bwa alignment tool support


New features in early beta testing:
1) BS-seq (methylation) analysis
2) Whole genome homology-guided assembly


Improvements:
1) Importer supports multiple input and output formats from Illumina GA2/HiSeq and Life Tech SOLiD 
2) Several new converters including e.g. SAM format support
3) Fixed a multitude of bugs (you better don't ask)

Compatibility:
Please use the following versions of third party tools
1) GenomeMapper version x or higher: http://1001genomes.org/downloads/genomemapper.html
2) bwa version 0.5.6 or higher: https://sourceforge.net/projects/bio-bwa/files/
3) bowtie version 1.12 or higher:
4) novoalign
5) Boost version 1.34.1 or higher
6) GNU Scientific library version 0.11 or higher

