AuditXP allows questions to be generated and assigned to barriers that have impact to the safety, regulations and any other management systems to ensure the integrity of barriers. Verify safety barrier performanceOnce safety barriers are implemented, their performance should be monitored.
AuditXP allows. Find out more. BowTieXP is unique in its ability to visualise complex risks in a way that is understandable, yet also allows for detailed risk based improvement plans. BowTieXP standard will get you started to identify and manage your risks.
BowTieXP standard will get you started to identify and manage your risks in 6. It is a semi-quantitative risk analysis methodology in which the frequency of a negative event is calculated according to the risk reduction delivered by the independent protection layers barriers. Click on on the specific product by method for the more information. It does not allow the user to edit or modify any of the content.
Benefits: Ideal for personnel who have to find and use the information in the Bowtie files Maintains content integrity Reporting capability All bowtie standard features accessible except editing. Using Microsoft Excel-compatible spreadsheets, this unique software has broken all the rules, giving you the freedom and flexibility to build and manipulate data in BowTie diagrams almost as freely as Excel will allow. Engage a global business with local experience and knowledge.
Smaller values make alignment slower but more senstive. Default: the --sensitive preset is used by default, which sets -L to 20 both in --end-to-end mode and in --local mode. Sets a function governing the interval between seed substrings to use during multiseed alignment. For instance, specifying -i S,1,2. See also: setting function options. If the function returns a result less than 1, it is rounded up to 1.
Default: the --sensitive preset is used by default, which sets -i to S,1,1. For instance, specifying -L,0,0. Reads exceeding this ceiling are filtered out. Default: L,0,0. Default: Default: 4. When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value.
This is also the default behavior when the input doesn't specify quality values e. If --nofw is specified, bowtie2 will not attempt to align unpaired reads to the forward Watson reference strand.
If --norc is specified, bowtie2 will not attempt to align unpaired reads against the reverse-complement Crick reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i. Default: both strands enabled. In this mode, Bowtie 2 requires that the entire read align from one end to the other, without any trimming or "soft clipping" of characters from either end.
The match bonus --ma always equals 0 in this mode, so all alignment scores are less than or equal to 0, and the greatest possible alignment score is 0.
This is mutually exclusive with --local. In this mode, Bowtie 2 does not require that the entire read align from one end to the other. Rather, some characters may be omitted "soft clipped" from the ends in order to achieve the greatest possible alignment score. The match bonus --ma is used in this mode, and the best possible alignment score is equal to the match bonus --ma times the length of the read. Specifying --local and one of the presets e. This is mutually exclusive with --end-to-end.
Sets the match bonus. Not used in --end-to-end mode. Default: 2. Sets the maximum MX and minimum MN mismatch penalties, both integers. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N.
If --ignore-quals is specified, the number subtracted quals MX. Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N. Default: 1. Default: 5, 3. Sets a function governing the minimum alignment score needed for an alignment to be considered "valid" i. This is a function of read length. For instance, specifying L,0, The default in --end-to-end mode is L, Only the best alignment is reported.
Increasing -M makes bowtie2 slower, but increases the likelihood that it will pick the correct alignment for a read that aligns many places.
See also: reporting. The default is 3 in --end-to-end mode and 2 in --local mode. All alignments found are reported in descending order by alignment score. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates.
Note: Bowtie 2 is not particularly designed with large -k in mind, and when aligning reads to long, repetitive genomes large -k can be very, very slow. Like -k but with no upper limit on number of alignments to search for. Note: Bowtie 2 is not particularly designed with -a mode in mind, and when aligning reads to long, repetitive genomes this mode can be very, very slow. A seed extension "fails" if it does not yield a new best or a new second-best alignment.
This limit is automatically adjusted up when -k or -a are specified. When "re-seeding," Bowtie 2 simply chooses a new set of reads same length, same number of mismatches allowed at different offsets and searches for more alignments.
A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than The minimum fragment length for valid paired-end alignments. A bp gap would not be valid in that case.
If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. The maximum fragment length for valid paired-end alignments. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.
Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. Default: --fr appropriate for Illumina's Paired-end Sequencing Assay. By default, when bowtie2 cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior.
By default, bowtie2 looks for discordant alignments if it cannot find any concordant alignments. If the mates "dovetail", that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. See also: Mates can overlap, contain or dovetail each other.
Default: mates cannot dovetail in a concordant alignment. If one mate alignment contains the other, consider that to be non-concordant.
Default: a mate can contain the other in a concordant alignment. If one mate alignment overlaps the other at all, consider that to be non-concordant. Default: mates can overlap in a concordant alignment. Print the wall-clock time required to load the index files and align the reads. This is printed to the "standard error" "stderr" filehandle.
If --un-gz is specified, output will be gzip compressed. If --un-bz2 is specified, output will be bzip2 compressed. If --al-gz is specified, output will be gzip compressed. If --al-bz2 is specified, output will be bzip2 compressed. Having alignment metric can be useful for debugging certain problems, especially performance issues.
See also: --met. Default: metrics disabled. Write bowtie2 metrics to the "standard error" "stderr" filehandle. This is not mutually exclusive with --met-file. Only matters if either --met-stderr or --met-file are specified. Specify --sam-rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.
This reduces the memory footprint of the aligner but requires more time to calculate text offsets. Searching for alignments is highly parallel, and speedup is close to linear. Increasing -p increases Bowtie 2's memory footprint.
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