Release 2.0.0

bcgsc · Sep 1, 2016 · 92ffd21 · 92ffd21
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,55 @@
+2016-08-30  Ben Vandervalk <benv@bcgsc.ca>
+
+	* Release version 2.0.0
+	* New Bloom filter mode for assembly => assemble large genomes
+	with minimal memory (e.g. 34G for H. sapiens)
+	* Update param defaults for modern Illumina data
+	* Make sqlite3 an optional dependency
+
+	abyss-bloom:
+	* New 'compare' command for bitwise comparison of Bloom filters
+	(thanks to @bschiffthaler!)
+	* New 'kmers' command for printing k-mers that match a Bloom filter
+	(thanks to @bschiffthaler!)
+
+	abyss-bloom-dbg:
+	* New preunitig assembler that uses Bloom filter
+	* Add 'B' param (Bloom filter size) to 'abyss-pe' command to enable
+	Bloom filter mode
+	* See README.md and '--help' for further instructions
+
+	abyss-fatoagp:
+	* Mask scaftigs shorter than 50bp with 'N's (short scaftigs
+	were causing problems with NCBI submission)
+
+	abyss-pe:
+	* Update default parameter values for modern Illumina data
+	* Change 'l=k' => 'l=40'
+	* Change 's=200' => 's=1000'
+	* Change 'S=s' => 'S=1000-10000' (do a param sweep of 'S')
+	* Use 'DistanceEst --mean' for scaffolding stage, instead of
+	the default '--mle'
+
+	abyss-sealer:
+	* New '--max-gap-length' ('-G') option to replace unintuitive
+	'--max-frag'; use of '--max-frag' is now deprecated
+	* Require user to explicitly specify Bloom filter size (e.g.
+	'-b40G')
+	* Report false positive rate (FPR) when building/loading Bloom
+	filters
+	* Don't require input FASTQ files when using pre-built Bloom
+	filter files
+
+	konnector:
+	* Fix bug causing output read 2 file to be empty
+	* New percent sequence identity options ('-x' and '-X')
+	* New '--alt-paths-mode' option to output alternate connecting
+	paths between read pairs
+
+	README.md:
+	* Fixes to documentation of ABYSS and abyss-pe parameters
+	(thanks to @nsoranzo!)
+
 2015-05-28  Ben Vandervalk <benv@bcgsc.ca>
 
 	* Release version 1.9.0

diff --git a/bin/abyss-pe b/bin/abyss-pe
@@ -348,7 +348,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 1.9.0"
+	@echo "abyss-pe (ABySS) 2.0.0"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

diff --git a/configure.ac b/configure.ac
@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 1.9.0, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.0.0, 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
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 1.9.0" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.0.0" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 1.9.0" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.0.0" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1
@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 1.9.0" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.0.0" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br

diff --git a/doc/flowchart.graffle b/doc/flowchart.graffle
@@ -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 1.9.0}</string>
+\f0\b\fs28 \cf0 ABySS paired-end pipeline version 2.0.0}</string>
 				<key>VerticalPad</key>
 				<integer>0</integer>
 			</dict>