SHORE Files

Release Notes for SHORE version 0.9
===================================

v0.9.3
------

- fix backwards compatibility with g++ 4.1.2

v0.9.2
------

- g++ 4.8 compatibility fix
- fix configure issue (required for Ubuntu 13)

v0.9.1
------

- g++ 4.7 compatibility fix

v0.9.0
------

- preprocess, mapflowcell: updated user interface,
                           added bowtie2,
                           dropped NovoAlign and GSnap due to lack of maintenance.


Release Notes for SHORE version 0.8
===================================

v0.8.1
------

 - fixes a compile/install bug
 - fixes a 'shore consensus' issue in combination with correct4pe overlap correction

v0.8.0
------

 - readsfl format
    - optional column of 3-char tags (~ TAG:value;TAG:value;...;) following the
      quality(ies)
      valid tags:
        - BAD (bad quality state, int)
        - BAR (resolved barcode sequence, string)
        - CLL (left clip position, int)
        - CLR (right clip position, int)
        - DST (read has an alignment with the given edit distance, int)
        - RGR (read group, string)
        - ORI expected orientation relative to read1 (<>,><,>>)
        - NUM number of (non-technical) reads for the template (default 2 for
              non-single reads, mandatory for >2 non-technical reads)
    - optional single character attribute as prefix for the pe index:
        - f     filter orphan: partner lost due to quality filtering
        - t     technical read, e.g. barcode read
        - p     paired read, not 'f' or 't'

 - maplist format
    - optional column of 3-char tags (~ TAG:value;TAG:value;...) following the
      quality(ies)
      valid tags:
        - MPQ (mapping quality, int)
        - RGR (read group, string)
        - NUM number of reads for the template (default 2 for non-single reads,
              mandatory for >2 non-technical reads)
        - ORI expected orientation relative to read1 (<>,><,>>)
        - NXP mapping position of the next read of the template ([0-9]+:[0-9]+[DP]),
              valid if read is concordant or partner has a single mapping pos
    - optional single character attribute as prefix for the pe index, replaces
      previous encoding of pe info:
        - f     filter orphan: partner lost due to quality filtering
        - t     technical read, e.g. barcode read
        - p     paired read, not 'f' or 't', but any of the below
        - c     concordant: forms a likely pairing with it's partner, given the
                insert size distribution (does not guarantee this is the most
                likely pairing given repeats with variable length! Does it make
                sense to discriminate? Or store more info in a tag?)
        - d     discordant: neither this mapping of the read, nor any other can
                participate in a likely pairing, given the insert size distribution
        - b     suboptimal: concordant, but another mapping of the read can form
                a more likely pairing with the same partner
        - a     accessory hit: discordant, and other mappings of the read are
                concordant
        - o     mapping orphan: partner is unmapped

 - import
    - support multiple barcode reads and barcodes with different lengths, -w option
      replaced with additional columns in the barcode sheet
    - a library/sample identifier must now be specified either via -i or -r
    - --nondestructive now uses tags, can be used for console exporter as well

 - mapflowcell
    - default for --upgrade (-P) is now 'replace'
    - GenomeMapper 0.4.4 required (unlimited read length and mismatches, new pe flag)
 
 - correct4pe
    - now sets the NXP tag
    - uses new pe index format
    - library identifier is now a string, already set in import (RGR tag), -e option removed
    - option for cutting overlapping pair alignments

 - SAM output
    - use new paired end information tags to set the mate information

 - qVar
    - support all alignment string features
    - bug fixes

  - alignment filters
    - new paired end joining options -Y and -U for PE support in coverage, peak etc.

 - mapdisplay
    - paired end support using -Y, -U
    - SVG output support

 - Support lzma (xz) compression
    - default compression can be selected, e.g. "shore -Z gz import ..."
    - liblzma dependency can be passed by with "./configure --without-lzma"

 - Sources
    - all C++ sources are now below the src/ directory
    - core functionality is now below src/CoreLib/shore and compiled into a
      separate library (libshore.so/libshore.a).
    - use the GNU autotools build system

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