From 271197abce5d56f5111e9f33b1828cb4346cdc42 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 27 Sep 2024 10:22:00 +0200 Subject: [PATCH] [WIP] --- src/bowtie2/align/config.vsh.yaml | 4 ++++ src/bowtie2/align/help.txt | 22 +++++++++++----------- 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/src/bowtie2/align/config.vsh.yaml b/src/bowtie2/align/config.vsh.yaml index c62eb6e0..b713054b 100644 --- a/src/bowtie2/align/config.vsh.yaml +++ b/src/bowtie2/align/config.vsh.yaml @@ -82,6 +82,10 @@ functionality: description: trim bases from 3'/right end of reads (0) type: integer default: 0 + - name: --trim-to + description: "[3:|5:] trim reads exceeding bases from either 3' or 5' end. If the read end is not specified then it defaults to 3 (0)" + type: string + - name: phred resources: diff --git a/src/bowtie2/align/help.txt b/src/bowtie2/align/help.txt index a8063541..0f994408 100644 --- a/src/bowtie2/align/help.txt +++ b/src/bowtie2/align/help.txt @@ -20,7 +20,7 @@ Usage: Options (defaults in parentheses): - Input: + ###Input: -q query input files are FASTQ .fq/.fastq (default) --tab5 query input files are TAB5 .tab5 --tab6 query input files are TAB6 .tab6 @@ -41,7 +41,7 @@ Options (defaults in parentheses): --phred64 qualities are Phred+64 --int-quals qualities encoded as space-delimited integers - Presets: Same as: + ###Presets: Same as: For --end-to-end: --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 @@ -54,7 +54,7 @@ Options (defaults in parentheses): --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 - Alignment: + ###Alignment: -N max # mismatches in seed alignment; can be 0 or 1 (0) -L length of seed substrings; must be >3, <32 (22) -i interval between seed substrings w/r/t read len (S,1,1.15) @@ -70,7 +70,7 @@ Options (defaults in parentheses): OR --local local alignment; ends might be soft clipped (off) - Scoring: + ###Scoring: --ma match bonus (0 for --end-to-end, 2 for --local) --mp max penalty for mismatch; lower qual = lower penalty (6) --np penalty for non-A/C/G/Ts in read/ref (1) @@ -79,18 +79,18 @@ Options (defaults in parentheses): --score-min min acceptable alignment score w/r/t read length (G,20,8 for local, L,-0.6,-0.6 for end-to-end) - Reporting: + ###Reporting: (default) look for multiple alignments, report best, with MAPQ OR -k report up to alns per read; MAPQ not meaningful OR -a/--all report all alignments; very slow, MAPQ not meaningful - Effort: + ###Effort: -D give up extending after failed extends in a row (15) -R for reads w/ repetitive seeds, try sets of seeds (2) - Paired-end: + ###Paired-end: -I/--minins minimum fragment length (0) -X/--maxins maximum fragment length (500) --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) @@ -100,14 +100,14 @@ Options (defaults in parentheses): --no-contain not concordant when one mate alignment contains other --no-overlap not concordant when mates overlap at all - BAM: + ###BAM: --align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads. Use this option to align paired-end reads instead. --preserve-tags Preserve tags from the original BAM record by appending them to the end of the corresponding SAM output. - Output: + ###Output: -t/--time print wall-clock time taken by search phases --un write unpaired reads that didn't align to --al write unpaired reads that aligned at least once to @@ -135,12 +135,12 @@ Options (defaults in parentheses): --sam-append-comment Append FASTA/FASTQ comment to SAM record - Performance: + ###Performance: -p/--threads number of alignment threads to launch (1) --reorder force SAM output order to match order of input reads --mm use memory-mapped I/O for index; many 'bowtie's can share - Other: + ###Other: --qc-filter filter out reads that are bad according to QSEQ filter --seed seed for random number generator (0) --non-deterministic