software:topical:lifescience:ngs_read_mapping_tools

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
software:topical:lifescience:ngs_read_mapping_tools [2018/12/13 11:45]
meesters
software:topical:lifescience:ngs_read_mapping_tools [2019/10/24 15:48]
meesters [BarraCuda]
Line 1: Line 1:
 ====== NGS Read Mapping Software on Mogon ====== ====== NGS Read Mapping Software on Mogon ======
  
-As a first introduction into NGS alignment software tools we recommend reading this short [[https://www.ecseq.com/support/ngs/what-is-the-best-ngs-alignment-software|blog post]]. Or in other words: It might be, that the list of supported tools grows and grows, [[https://hpc.uni-mainz.de/high-performance-computing/service-angebot/softwareinstallation/|due to your requests]], but will never really cover everybody's favorite tool.+As a first introduction into NGS alignment software tools we recommend reading this short [[https://www.ecseq.com/support/ngs/what-is-the-best-ngs-alignment-software|blog post]]. Or in other words: It might be, that the list of supported tools grows and grows, [[https://hpc.uni-mainz.de/high-performance-computing/service-angebot/softwareinstallation/|due to your requests]], but will never really cover everybody's favorite tool - there are just too many and some are just not worth having.
  
-Notwithstanding, own [[software:topical:lifescience:ngs_read_mapping_tools#Comparison_Benchmarks|benchmarks]] a first impression can be found in [[http://www.ecseq.com/support/benchmark.html|the same blog]]. 
 ===== Software Options ===== ===== Software Options =====
  
Line 12: Line 11:
 ''bio/BWA/<version>'' ''bio/BWA/<version>''
  
-=== The Wrapper Script ===+You can find a wrapper to ease your workflow, [[software:topical:lifescience:#standard_mappers|below]].
  
-To leverage the task from 1 (or a few) samples to be mapped to several in parallel, we provide a wrapper script, which is available as a module:  
- 
-''bio/parallel_BWA'' 
- 
-The code is under version management and hosted [[https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis|internally, here]]. 
- 
-<WRAP center round important 90%> 
-The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one. 
-</WRAP> 
- 
-Calling ''parallel_BWA -h'' will display a help message with all the options, the script provides. Likewise, the call ''parallel_BWA --credits'' will display credits and a version history. 
- 
-The script, after loading the module, can then be run like: 
- 
-<code bash> 
-$ parallel_BWA [options] <referencedir> <inputdir> 
-</code> 
- 
-<WRAP center round important 90%> 
-**Limitations**: 
- 
-  * The wrapper recognizes FASTQ files with suffixes "''*.gz''", "''*.fastq''" or "''*.fq''" and will allways assume FASTQ files (compressed or uncompressed). 
-  * The number of processes (and therefore nodes) is limited to the number of samples. 
-  * The wrapper only works for paired end sequencing data, where the file tuples are designated with the following strings "''_1''" and "''_2''" or "''_R1''" and "''_R2''", respectively. 
-  * BWA does not scale well to big data. It is better to split input to chuncks of ~1GB (take this with a grain of salt: there are not scaling tests, yet) 
-  * BWA does not scale well beyond a NUMA block (8 threads on Mogon I) 
-  * There are only a few options, as internally the wrapper calls ''bwa mem'' (or ''bwa aln'' in the single end case) and only sets up a few things to yield performance. 
-</WRAP> 
- 
-About Arguments: 
- 
-  * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference 
-  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:trimmomatic|trimmomatic module]]. 
- 
-The options: 
-  * ''parallel_BWA'' attempts to deduce your SLURM account. This may fail, in which case ''-A, --account'' needs to be supplied. 
-  * ''-N,--nodes'' allows to reserve more than 1 node (the default). This may speed up the screening; see the limitations above. 
-  * ''-d,--dependency'', list of comma separated jobids, the job will wait for to finish 
-  * ''-l,--runlimit'', this defaults to 300 minutes. 
-  * ''-p,--partition'', the default is ''nodeshort'' or ''parallel'' on Mogon2, no smp-partition should be choosen. 
-  * ''-t,--threads'', BWA can work in parallel. Please consult the manual. The default is 8. 
-  * ''-o,--outdir'' output directory path (default is the current working directory) 
-  * ''--single'' (no arguments) to evaluate single end data 
-  * ''--args'' to supply additional flags, e. g. ''--args="-l 1024 -n 0.02"'' for BWA - note the quotation marks, they are necessary. 
-   
-Output: 
- 
-  * Per input tuple (paired sequencing data, only) a BAM file with the prefix of the input will be written. In the case of single end data, there will be one output per input, only. 
  
 ==== BarraCuda ==== ==== BarraCuda ====
Line 73: Line 24:
 See [[:software:topical:lifescience:ngs_read_mapping_tools#gpu-based|below for a wrapper script]] to ease your workflow. See [[:software:topical:lifescience:ngs_read_mapping_tools#gpu-based|below for a wrapper script]] to ease your workflow.
  
 +==== Minimap2 ====
 +
 +[[https://github.com/lh3/minimap2|Minimap2]] is supposed to be a replacement for ''bwa mem''. Modules are installed under 
 +
 +''bio/minimap2''
  
  
Line 81: Line 37:
 ''bio/SeqAn/<version>'' ''bio/SeqAn/<version>''
  
-You can find a wrapper to ease your workflow, [[software:topical:lifescience:#standard_mappers|below]], eventually ((not yet)).+You can find a wrapper to ease your workflow, [[software:topical:lifescience:#standard_mappers|below]].
  
  
Line 87: Line 43:
  
 [[https://www.nature.com/articles/nmeth.1923|Bowtie2]] is a well known read aligner with a focus on gapped alignments. [[https://www.nature.com/articles/nmeth.1923|Bowtie2]] is a well known read aligner with a focus on gapped alignments.
 +
 +Module(s) can be found at:
 +
 +''bio/Bowtie2/<version>''
 +
 +You can find a wrapper to ease your workflow, [[software:topical:lifescience:#standard_mappers|below]].
  
 ==== STAR ==== ==== STAR ====
  
-<WRAP center round todo 65%>  +[[https://www.ncbi.nlm.nih.gov/pubmed/23104886|STAR]] is a well known mapping tool for RNA-Seq data.  
-More info soon-ish+ 
-</WRAP>+Module(s) can be found at: 
 + 
 +''bio/STAR/<version>'' 
 + 
 +You can find a wrapper to ease your workflow, [[software:topical:lifescience:#standard_mappers|below]].
  
 ==== segemehl ==== ==== segemehl ====
Line 106: Line 72:
 ''bio/segemehl/0.2.0-foss-2018a'' ''bio/segemehl/0.2.0-foss-2018a''
  
 +==== TopHat ====
 +
 +[[https://ccb.jhu.edu/software/tophat/index.shtml|TopHat]] is a fast splice junction mapper for RNA-Seq reads.
 +
 +Module can be found at:
 +
 +''bio/TopHat/<version>''
 +
 +
 +<WRAP center round info 90%>
 +This program is not yet incorporated into the wrapping module.
 +</WRAP>
 ==== yara ==== ==== yara ====
  
Line 121: Line 99:
  
 Most mapping tools adhere to this paradigm: They work on a reference (directory). They are, therefore, easily wrapped, such that the reference can be staged-in to a node-local directory (e.g. a [[:ramdisk|ramdisk]]) in order to avoid random I/O (and consequently prolonged run times) on the parallel file system. Most mapping tools adhere to this paradigm: They work on a reference (directory). They are, therefore, easily wrapped, such that the reference can be staged-in to a node-local directory (e.g. a [[:ramdisk|ramdisk]]) in order to avoid random I/O (and consequently prolonged run times) on the parallel file system.
 +
 +
 +Now, to leverage the task from 1 (or a few) samples to be mapped to several in parallel, we provide a wrapper script, which is available as a module: 
 +
 +''bio/parallel_MappingTools''
 +
 +The code is under version management and hosted [[https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis|internally, here]].
 +
 +<WRAP center round important 90%>
 +The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one.
 +</WRAP>
 +
 +Calling ''MapperWrapper -h'' will display a help message with all the options, the script provides. Likewise, the call ''MapperWrapper --credits'' will display credits and a version history.
 +
 +The script, after loading the module, can then be run like:
 +
 +<code bash>
 +$ MapperWrapper --executable=<executable> [options] <referencedir> <inputdir>
 +</code>
 +
 +<WRAP center round important 90%>
 +**Considerations**:
 +
 +  * The wrapper recognizes FASTQ files with suffixes "''*.gz''", "''*.fastq''" or "''*.fq''" and will always assume FASTQ files (compressed or uncompressed). [[software:topical:lifescience:#yara|yara]] accepts bzipped files, too.
 +  * The number of processes (and therefore nodes) is limited to the number of samples.
 +  * The wrapper only works for paired end sequencing data, where the file tuples are designated with the following strings "''_1''" and "''_2''" or "''_R1''" and "''_R2''", respectively.
 +  * There are only a few options, as internally the wrapper calls ''bwa mem'' (or ''bwa aln'' in the single end case) and only sets up a few things to yield performance. Likewise a switch for single and paired end data exists for other mappers.
 +</WRAP>
 +
 +About Arguments:
 +
 +  * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference
 +  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:qc|quality check module]].
 +
 +The options:
 +  * ''MapperWrapper'' attempts to deduce your SLURM account. This may fail, in which case ''-A, --account'' needs to be supplied.
 +  * ''--verbose,--no-verbose''  verbose execution (off by default)
 +  * ''--executable''  mandatory argument to designate the executable possible arguments: ''bwa'', ''bowtie2'', ''yara''
 +  * ''-d,--dependency'', list of comma separated jobids, the job will wait for to finish
 +  * ''-l,--runlimit'', this defaults to 300 minutes.
 +  * ''-p,--partition'', the default is ''nodeshort'' or ''parallel'' on Mogon2, no smp-partition should be choosen.
 +  * ''-o,--outdir'' output directory path (default is the current working directory)
 +  * ''--tag'' optional tag/prefix for logfiles and directories
 +  * ''--groups'' set to provide a lists of read group tags (len(groups) must equal to No. of files)
 +  * ''--single'' (no arguments) to evaluate single end data
 +  * ''--args'' to supply additional flags, e. g. ''--args="-l 1024 -n 0.02"'' for BWA - note the quotation marks, they are necessary.
 +  
 +Output:
 +
 +  * Per input tuple (paired sequencing data, only) a BAM file with the prefix of the input will be written. In the case of single end data, there will be one output per input, only.
 +
 +=== Generating Read Group Tags ===
 +
 +Read group tags can be inserted with the ''--groups'' flag((From version 0.6 onward.)). The tags are supplied as a list on the command line. An example code to generate a tag list for consecutively ordered tags would be:
 +
 +<code bash>
 +# defining the input directory appropriately in a master script:
 +inputdir=/some/path/to/your/data # assuming '_R1' defines the forward reads in a paired end scenario
 +
 +# a template - may deviate from project to project
 +template="@RG\tID:+ID+\tLB:unknown_lb\tPL:illumina\tSM:sample+ID+"
 +# the tag list to be generated
 +tags=""
 +# number of samples - this snippet could be integrated in a script 
 +nsamples=$(find $inputdir -name '*_R1*.fastq' | grep -v unpaired | wc -l)
 +# now the actual generation:
 +for ((i=1; i <= $nsamples; i++)); do
 +  tags="$tags $(sed -e "s/+ID+/$i/g" <<< $template)"
 +done
 +</code>
  
  
Line 140: Line 188:
  
 <WRAP center round important 90%> <WRAP center round important 90%>
-**Limitations**: +**Considerations**: 
-  * See the parallel_BWA wrapper +  * See the [[software:topical:lifescience:ngs_read_mapping_tools#standard_mappers|"standard" Mappers]] 
-  * Also: The script will only use the ''m2_gpu'' partition and therefore needs an account with the ''m2_'' prefix.+  * Also: The script will only use the ''m2_gpu'' partition and therefore needs an account with the ''m2_'' prefix((This is because development to support the wild "zoo" of hardware and partition setting is hardly worth the effort for this software, as tests show that standard bwa (properly mapped) outperforms the gpu version.)).
 </WRAP> </WRAP>
  
Line 148: Line 196:
 About Arguments: About Arguments:
   * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference. No symbolic links are allowed.   * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference. No symbolic links are allowed.
-  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:trimmomatic|trimmomatic module]].+  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:qc|quality check module]].
  
  
Line 162: Line 210:
  
 ===== Comparison Benchmarks ===== ===== Comparison Benchmarks =====
 +
 +
 +Notwithstanding, own [[software:topical:lifescience:ngs_read_mapping_tools#Comparison_Benchmarks|benchmarks]] a first impression can be found in [[http://www.ecseq.com/support/benchmark.html|the same blog]].
  
 <WRAP center round todo 65%> <WRAP center round todo 65%>
 This part needs some more time to be finished .... This part needs some more time to be finished ....
 </WRAP> </WRAP>