diff --git a/ChangeLog b/ChangeLog index 589c8a481..8316e1c56 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,45 @@ +2015-05-28 Ben Vandervalk + + * Release version 1.9.0 + * New paired de Bruijn graph mode for assembly. + * First official release of Sealer, a tool for closing + scaffold gaps by navigating a Bloom filter de Bruijn graph. + * New outward extension feature for Konnector to generate + long pseudo-reads. + * Support for the DIDA (Distributed Indexing Dispatched + Alignment) framework, for computing sequence alignments + in parallel across multiple machines. + * Unit tests can now be run easily with 'make check', without + external dependencies. + + abyss-bloom: + * abyss-bloom 'build' command now supports -j option for + multi-threaded Bloom filter construction. + + abyss-map: + * New --protein option for mapping protein sequences. + + abyss-pe: + * New paired de Bruijn graph mode for assembly. Enable by + setting `k` to the k-mer pair span and `K` to size of an + individual k-mer in a k-mer pair. See README.md for further + details. + * New `aligner=dida` option for using the DIDA parallel alignment + framework. See the DIDA section of the abyss-pe man page + for usage details. + * New `graph=gfa` option to use the GFA (Graphical + Fragment Assembly) format for intermediate graph files. + + abyss-sealer: + * New tool for closing scaffold gaps by navigating a Bloom + filter de Bruijn graph + * See Sealer/README.md or abyss-sealer man page for details + and examples. + + konnector: + * New --extend option for extending merged and unmerged + reads outwards in the de Bruijn graph. + 2014-07-09 Anthony Raymond * Release version 1.5.2 diff --git a/bin/abyss-pe b/bin/abyss-pe index ff21d7a36..60436c610 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -318,7 +318,7 @@ Report bugs to .\n' version: @printf '\ -abyss-pe (ABySS) 1.5.2\n\ +abyss-pe (ABySS) 1.9.0\n\ Written by Shaun Jackman and Anthony Raymond.\n\ \n\ Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n' diff --git a/configure.ac b/configure.ac index 8fbfb04ee..a3af48837 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 1.5.2, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 1.9.0, abyss-users@bcgsc.ca, abyss, http://www.bcgsc.ca/platform/bioinfo/software/abyss) m4_include(m4/m4_ax_pthread.m4) AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects) diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index ce3b3fb08..6b9024056 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2014-May" "ABYSS (ABySS) 1.5.2" "User Commands" +.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 1.9.0" "User Commands" .SH NAME ABYSS \- assemble short reads into contigs .SH SYNOPSIS @@ -94,4 +94,4 @@ Written by Jared Simpson and Shaun Jackman. .SH "REPORTING BUGS" Report bugs to . .SH COPYRIGHT -Copyright 2014 Canada's Michael Smith Genome Sciences Centre +Copyright 2015 Canada's Michael Smith Genome Sciences Centre diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1 index 08df080b6..349ee054b 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2014-May" "abyss-pe (ABySS) 1.5.2" "User Commands" +.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 1.9.0" "User Commands" .SH NAME abyss-pe - assemble reads into contigs .SH SYNOPSIS @@ -311,4 +311,4 @@ Written by Shaun Jackman. .SH "REPORTING BUGS" Report bugs to . .SH COPYRIGHT -Copyright 2014 Canada's Michael Smith Genome Sciences Centre +Copyright 2015 Canada's Michael Smith Genome Sciences Centre diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1 index 1d8e9eca0..e997080bf 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2014-May" "ABySS 1.5.2" "User Commands" +.TH abyss-tofastq "1" "2015-May" "ABySS 1.9.0" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br @@ -18,4 +18,4 @@ Written by Shaun Jackman. .SH "REPORTING BUGS" Report bugs to . .SH COPYRIGHT -Copyright 2014 Canada's Michael Smith Genome Sciences Centre +Copyright 2015 Canada's Michael Smith Genome Sciences Centre diff --git a/doc/flowchart.graffle b/doc/flowchart.graffle index fa3d8975a..c00b8370b 100644 --- a/doc/flowchart.graffle +++ b/doc/flowchart.graffle @@ -5198,7 +5198,7 @@ {\colortbl;\red255\green255\blue255;} \pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural\qc -\f0\b\fs28 \cf0 ABySS paired-end pipeline version 1.5.2} +\f0\b\fs28 \cf0 ABySS paired-end pipeline version 1.9.0} VerticalPad 0