diff --git a/ChangeLog b/ChangeLog index 422a8c8e6..4f93b2d74 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,60 @@ +2014-05-01 Anthony Raymond + + * Release version 1.5.0 + * Assemble strand-specific RNA-Seq libraries into strand-specific + contigs. + * New parameters, Q and xtip. Improves assembly in high-coverage + regions by removing recurrent read errors. + * Portability fixes for Fujitsu C Compiler. + + abyss-pe: + * New parameter, `Q`, to mask low quality bases to N. + * New parameter, `xtip=1`, to remove 2-in 0-out tips. + * New parameter, `ss=1`, to perform strand-specific assembly + using ssRNA-Seq libraries. + * New command, `scaftigs`. Breaks scaffold sequences at 'N's and + produce a scaftigs.fa file. + * Include long-scaffs.fa in FAC statistics if `long` parameter + used. + + abyss-fixmate: + * Performance improvement for GCC-4.6 and older. + + DistanceEst: + * Report an estimation of duplicate fragments from read pairs + mapping to different contigs. + + abyss-fixmate: + * Report number of fragments removed as noise and outliers. + + ABYSS/ABYSS-P: + * New option, --SS, to support strand-specific assembly. + + abyss-layout: + * New option, --SS, to support strand-specific assembly. + + abyss-map: + * New option, --SS, to support strand-specific assembly. + + abyss-overlap: + * New option, --SS, to support strand-specific assembly. + + abyss-PathOverlap: + * New option, --SS, to support strand-specific assembly. + + abyss-scaffold: + * New option, --SS, to support strand-specific assembly. + * Don't prune xtips when scaffolding. + + AdjList: + * New option, --SS, to support strand-specific assembly. + + Overlap: + * New option, --SS, to support strand-specific assembly. + + PopBubbles: + * New option, --SS, to support strand-specific assembly. + 2013-11-20 Anthony Raymond * Release version 1.3.7 diff --git a/bin/abyss-pe b/bin/abyss-pe index d9e79e2b2..6c828eef0 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -1,6 +1,7 @@ #!/usr/bin/make -rRf # Run the ABySS assembler. -# Written by Shaun Jackman . +# Written by Shaun Jackman and +# Anthony Raymond . # Set pipefail to require that all commands of a pipe must succeed. SHELL=/bin/bash -o pipefail @@ -263,8 +264,8 @@ Report bugs to .\n' version: @printf '\ -abyss-pe (ABySS) 1.3.7\n\ -Written by Shaun Jackman.\n\ +abyss-pe (ABySS) 1.5.0\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 3f0de8b87..beb7efbd9 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 1.3.7, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 1.5.0, abyss-users@bcgsc.ca, abyss, http://www.bcgsc.ca/platform/bioinfo/software/abyss) AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects) AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp]) diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index 2815b4527..461a737b5 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2013-Nov" "ABYSS (ABySS) 1.3.7" "User Commands" +.TH ABYSS "1" "2014-May" "ABYSS (ABySS) 1.5.0" "User Commands" .SH NAME ABYSS \- assemble short reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1 index 95f952d82..8960eaea8 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2013-Nov" "abyss-pe (ABySS) 1.3.7" "User Commands" +.TH abyss-pe "1" "2014-May" "abyss-pe (ABySS) 1.5.0" "User Commands" .SH NAME abyss-pe - assemble reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1 index 66d7e1ccc..68d553f00 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2013-Nov" "ABySS 1.3.7" "User Commands" +.TH abyss-tofastq "1" "2014-May" "ABySS 1.5.0" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br diff --git a/doc/flowchart.graffle b/doc/flowchart.graffle index e39d4ddac..a832eb046 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 1.3.6} +\f0\b\fs28 \cf0 ABySS paired-end pipeline version 1.5.0} VerticalPad 0 @@ -8382,7 +8382,7 @@ MasterSheets ModificationDate - 2013-09-19 18:10:26 +0000 + 2014-05-01 22:25:41 +0000 Modifier Tony Raymond NotesVisible @@ -8413,7 +8413,7 @@ NSPaperName string - B75A40CE-5BEE-4C78-A6CE-A00AA144D84B + 69FD0149-2077-40BA-84CF-28739E407FEB NSPaperSize @@ -8482,7 +8482,7 @@ SidebarWidth 120 VisibleRegion - {{-12, 0}, {1121, 778}} + {{-4, 0}, {1107, 794}} Zoom 1 ZoomValues diff --git a/doc/flowchart.pdf b/doc/flowchart.pdf index a59c16c9a..910a6d9dc 100644 Binary files a/doc/flowchart.pdf and b/doc/flowchart.pdf differ