From e78e95e2a304115249917d007377ac0fe239d483 Mon Sep 17 00:00:00 2001 From: Alexey Gurevich Date: Mon, 6 Aug 2018 12:50:51 +0300 Subject: [PATCH] Docs: fixed hyphens in CHANGES.txt --- CHANGES.txt | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/CHANGES.txt b/CHANGES.txt index 46e7203c80..49fb189f77 100644 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -25,48 +25,48 @@ specified with "--k-mer-size" option. 4. Improved and extended gene prediction/annotation functionality: - — Barrnap for rRNA genes prediction ("--rna-finding") is added; - — BUSCO for finding conserved single-copy orthologs ("--conserved-genes-finding"; + - Barrnap for rRNA genes prediction ("--rna-finding") is added; + - BUSCO for finding conserved single-copy orthologs ("--conserved-genes-finding"; Linux only) is added; - — regular predicted genes (using GeneMark or Glimmer) are split into full and partial; - — "--fungus" option is added for more accurate processing of fungus assemblies using + - regular predicted genes (using GeneMark or Glimmer) are split into full and partial; + - "--fungus" option is added for more accurate processing of fungus assemblies using GeneMark-ES and BUSCO; - — "--features" option is added to replace "-G/--genes", it allows to count all genomic + - "--features" option is added to replace "-G/--genes", it allows to count all genomic features from GFF or any specific feature type (e.g., 'CDS'). 5. Icarus updates: - — changes in alignment viewers: + - changes in alignment viewers: * GC% track is added to the read coverage pane; * a button for highlighting all assembly misassemblies is added; * local misassemblies are now unchecked (hidden) by default. - — static Circos plot of alignments ("--circos") is added; - — chromosome names in the main menu are sorted in the human-friendly order now + - static Circos plot of alignments ("--circos") is added; + - chromosome names in the main menu are sorted in the human-friendly order now (e.g., chr1, chr2, ..., chr10 instead of chr1, chr10, chr2, ...). 6. Improved reads support: - — reads are now mapped to all assemblies and various alignment stats are reported; - — single ("--single") and interlaced ("--12") reads are supported; - — multiple read libraries are supported, including both paired-end ("--pe1/2/12") + - reads are now mapped to all assemblies and various alignment stats are reported; + - single ("--single") and interlaced ("--12") reads are supported; + - multiple read libraries are supported, including both paired-end ("--pe1/2/12") and mate-pair ("--mp1/2/12") libraries; - — Oxford Nanopores ("--nanopore") and PacBio SMRT ("--pacbio") are supported; - — ready SAM and BAM files can be provided both for reads mapped against assemblies + - Oxford Nanopores ("--nanopore") and PacBio SMRT ("--pacbio") are supported; + - ready SAM and BAM files can be provided both for reads mapped against assemblies ("--sam/bam") and reads mapped against the reference genome ("--ref-sam/bam"); - reads stats can still be skipped by using "--no-read-stats" option. 7. Modified processing of undefined nucleotides ('N'): - — reference Ns are excluded from Genome Fraction computation (100% if all ACGT bases + - reference Ns are excluded from Genome Fraction computation (100% if all ACGT bases are covered); - — assembly Ns are excluded from "Unaligned" and "partially unaligned length" + - assembly Ns are excluded from "Unaligned" and "partially unaligned length" computation; - — scaffold gaps are now defined as simply a gap between alignments having at least 10 + - scaffold gaps are now defined as simply a gap between alignments having at least 10 consecutive Ns (affects "# scaffold gap size mis.", previously it was underestimated due to a strict threshold on the percentage of Ns in the gap sequence). 8. MetaQUAST changes: - — trying to download next best match if a reference genome is not found in NCBI + - trying to download next best match if a reference genome is not found in NCBI (without references mode only); - link to the combined reference report is added to the main report HTML; - — sample summary reports (TXT, TEX, etc) are renamed to exclude special characters in + - sample summary reports (TXT, TEX, etc) are renamed to exclude special characters in the filenames ('#', '%', etc). 9. Changes and new metrics related to scaffold gap size misassemblies: @@ -84,9 +84,9 @@ misassembly-related metrics). 11. Changes in the list of embedded third-party tools: - — removed: GAGE, gnuplot; - — replaced: MUMmer and E-MEM (new: Minimap2), Manta (new: GRIDSS); - — added: BUSCO, Barrnap, KMC, Red. + - removed: GAGE, gnuplot; + - replaced: MUMmer and E-MEM (new: Minimap2), Manta (new: GRIDSS); + - added: BUSCO, Barrnap, KMC, Red. 12. Fixed several minor bugs.