From 92ffd218213d495c0732e561f0943eac6404462f Mon Sep 17 00:00:00 2001 From: Ben Vandervalk Date: Thu, 1 Sep 2016 10:40:05 -0700 Subject: [PATCH] Release 2.0.0 --- ChangeLog | 52 +++++++++++++++++++++++++++++++++++++++++++ bin/abyss-pe | 2 +- configure.ac | 2 +- doc/ABYSS.1 | 2 +- doc/abyss-pe.1 | 2 +- doc/abyss-tofastq.1 | 2 +- doc/flowchart.graffle | 2 +- 7 files changed, 58 insertions(+), 6 deletions(-) diff --git a/ChangeLog b/ChangeLog index 8316e1c56..adfe73834 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,55 @@ +2016-08-30 Ben Vandervalk + + * 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 * Release version 1.9.0 diff --git a/bin/abyss-pe b/bin/abyss-pe index a8854ffa0..b73c71e0d 100755 --- 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 index 1e0ece8c0..5240c78aa 100644 --- 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 index 6b9024056..f8ae91eed 100644 --- 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 index 011db4662..72dd6b868 100644 --- 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 index e997080bf..af49809a0 100644 --- 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 index c00b8370b..4cd126369 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 1.9.0} +\f0\b\fs28 \cf0 ABySS paired-end pipeline version 2.0.0} VerticalPad 0