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  • Sample SLURM Scripts
    .../, and can be copied from there. If you choose to copy one of these sample scripts, please make sure you understand what each <code>#SBATCH</code> directive b ...or communication between jobs, view [[Multi-Threaded & Message Passing Job Scripts]]
    11 KB (1,685 words) - 14:21, 4 October 2023
  • Amber Job Sample Scripts
    1 KB (171 words) - 21:18, 5 December 2022

Page text matches

  • SLURM Scripts
    #REDIRECT [[Amber Job Sample Scripts]]
    38 bytes (5 words) - 17:37, 26 June 2017
  • Bracken
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species.
    3 KB (402 words) - 19:01, 10 June 2022
  • PsiCLASS
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...s from among those encoded in the graph, based on the read support in each sample. <br>
    4 KB (480 words) - 15:00, 14 December 2022
  • PAML
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> * HPC_{{uc:{{#var:app}}}}_CTL - sample .ctl files directory
    3 KB (367 words) - 20:12, 12 August 2022
  • SEQPower
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> SEQPower provides statistical power analysis and sample size estimation for sequence-based association studies.
    2 KB (274 words) - 22:38, 21 August 2022
  • GTOOL
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...be subsetted are specified using the --g and --s options. The genotype and sample files should be in the format specified by the FILE FORMAT webpage.
    3 KB (319 words) - 12:51, 10 September 2020
  • Alfred
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read
    3 KB (294 words) - 19:29, 14 November 2022
  • Fastq-tools
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> *fastq-sample : randomly sample reads, with or without replacement
    3 KB (306 words) - 17:31, 10 June 2022
  • MetaMaps
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> It simultaenously carries out read assignment and sample composition estimation.
    3 KB (322 words) - 19:25, 14 December 2021
  • AMRPlusPlus
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...mple or set of samples. You may want to know what is contained within your sample or how abundant a given sequence is relative to another.
    3 KB (365 words) - 21:19, 6 December 2019
  • MaSuRCA
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> * HPC_{{uc:{{#var:app}}}}_CFG - sample configuration file directory
    3 KB (340 words) - 18:24, 18 August 2022
  • QDD
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...configuration file directory. Copy the '<code>set_qdd_default.ini</code>' sample configuration file to your working directory and adjust as needed.
    4 KB (485 words) - 20:08, 21 August 2022
  • PolyGembler
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...pping marker set to contigs, polyGembler infers contig haplotypes for each sample. Contig haplotypes are then used to infer linkage groups corresponding to c
    3 KB (344 words) - 13:45, 3 November 2020
  • Nvidia CUDA Toolkit
    |{{#vardefine:pbs|1}} <!--JOB SCRIPTS--> ==Sample GPU Batch Job Scripts==
    4 KB (543 words) - 13:44, 20 November 2023
  • FALCON
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...o set a memory limit on kmer search with -M. See [[FALCON_fc_large_run_cfg|sample SLURM fc_large_run.cfg]] for an example.
    3 KB (395 words) - 15:19, 15 August 2022
  • Strelka
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...analysis by accounting for possible tumor cell contamination in the normal sample. A final empirical variant re-scoring step using random forest models train
    3 KB (369 words) - 14:24, 10 October 2023
  • Saffrontree
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...7 house keeping genes. SaffronTree utilises all of the genomic data in the sample to create a visual representation of the clustering of the data. It support
    3 KB (400 words) - 17:17, 31 May 2022
  • SNPGenie
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...priate to sequence the pooled nucleic acid content of the virus in a blood sample from that host. Comparing πN and πS for a gene product, or comparing gene
    3 KB (423 words) - 18:41, 1 June 2022
  • Eukulele
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> # Metagenomic or metatranscriptomic sample files (unless using the provided sample data)
    4 KB (453 words) - 22:12, 8 March 2024
  • MANTA
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...small sets of diploid samples and somatic variants in matched tumor/normal sample pairs. There is experimental support for analysis of unmatched tumor sample
    3 KB (432 words) - 19:27, 10 June 2022
  • Clairvoyante
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...yante with a sample and call variant on another shows that Clairvoyante is sample agnostic and general for variant calling. A slim version of Clairvoyante wi
    4 KB (453 words) - 13:39, 15 August 2022
  • Reptile
    * HPC_REPTILE_CONF - Sample configuration files The available binaries and scripts include:
    3 KB (458 words) - 21:46, 21 August 2022
  • Guppy
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...U Access]] for more details on how to request GPUs on HiPerGator. Here's a sample Guppy GPU script you might want to use as a starting point:
    4 KB (506 words) - 21:07, 14 December 2022
  • TACO
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> TACO: Multi-sample transcriptome assembly from RNA-Seq
    2 KB (234 words) - 18:53, 1 June 2022
  • GROMACS
    |{{#vardefine:job|1}} <!--JOB SCRIPTS--> <!--Job Scripts-->
    4 KB (556 words) - 19:16, 5 January 2023
  • GroopM
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> extract population genomes from multi-sample metagenomic datasets.
    2 KB (263 words) - 21:20, 6 December 2019
  • CAVIAR
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> * HPC_{{uc:{{#var:app}}}}_EXE - sample data directory
    2 KB (275 words) - 21:17, 6 December 2019
  • NPhase
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...loidy agnostic tool developed in python which predicts the haplotypes of a sample that was sequenced by both long and short reads by aligning them to a refer
    2 KB (275 words) - 17:53, 15 August 2022
  • BIOM
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...biome) is designed to be a general-use format for representing biological sample by observation contingency tables. The BIOM format is designed for general
    2 KB (272 words) - 21:02, 6 December 2019
  • CellRanger-ARC
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin region
    3 KB (288 words) - 18:24, 12 August 2022
  • TraitRate
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> Sample input files are available at
    2 KB (292 words) - 16:54, 22 August 2022
  • MOABS
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...alignment, methylation calling, identification of hypomethylation for one sample and differential methylation for multiple samples, and other downstream ana
    2 KB (291 words) - 19:53, 12 August 2022
  • TPMcalculator
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...sequencing reads. The TPMCalculator output is comprised of four files per sample reporting the TPM values and raw read counts for genes, transcripts, exons
    2 KB (293 words) - 19:45, 1 June 2022
  • Vamb
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> .... It performs excellently with multiple samples, and pretty good on single-sample data. Vamb is implemented purely in Python (with a little bit of Cython) an
    3 KB (302 words) - 18:59, 1 February 2021
  • Resistome
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...a CSV formatted annotation database. The alignment file is treated as the sample resistome. This is done by counting each alignment for each target gene fou
    2 KB (297 words) - 21:46, 21 August 2022
  • BPP
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> Sample '.ctl' files are in the <code>'$HPC_BPP_CTL'</code> directory. You need to
    2 KB (294 words) - 18:21, 12 August 2022
  • LongQC
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc.
    2 KB (286 words) - 14:52, 12 October 2021
  • Mccortex
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant
    3 KB (297 words) - 22:22, 8 September 2020
  • Ngs-bits
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> * SampleGender - Determines sample gender based on a BAM file.
    3 KB (296 words) - 16:57, 10 June 2022
  • MetaCompare
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...or ARGs to be disseminated into human pathogens from a given environmental sample based on metagenomic sequencing data.
    3 KB (304 words) - 21:21, 6 December 2019
  • GPhoCS
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...e in a Bayesian manner, using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci.
    3 KB (300 words) - 21:20, 6 December 2019
  • Slurm
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...duling workloads whether those submitted directly to the scheduler via job scripts or behind the scenes of more convenient interfaces like [[Open OnDemand]],
    5 KB (763 words) - 17:37, 5 March 2024
  • Corset
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...ssion patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools
    3 KB (309 words) - 17:09, 10 June 2022
  • Jasmine
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, s
    3 KB (317 words) - 19:09, 15 August 2022
  • HASLR
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...her with Next Generation Sequencing reads (such as Illumina) from the same sample. HASLR is capable of assembling large genomes on a single computing node. O
    3 KB (315 words) - 19:53, 17 August 2020
  • Momi
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...MOran Models for Inference) is a Python package that computes the expected sample frequency spectrum (SFS), a statistic commonly used in population genetics,
    3 KB (305 words) - 19:03, 4 April 2022
  • DVGfinder
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...ms, ViReMa-a and DI-tector, in a unique workflow, making the analysis of a sample easier and more intuitive. Also, DVGfinder_v3 implements a Gradient Boostin
    3 KB (319 words) - 13:59, 31 July 2023
  • EMMAX
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA alg
    3 KB (304 words) - 15:06, 15 August 2022
  • AlphaFold
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ''Expand this section to view sample script for version 2.1.2.''
    6 KB (832 words) - 15:38, 2 February 2024
  • Saige
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->
    3 KB (297 words) - 19:29, 20 January 2023
  • REPdenovo
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> * HPC_{{uc:{{#var:app}}}}_EXE - sample directory
    3 KB (327 words) - 21:43, 21 August 2022
  • ContaVect
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> The sample config file can be copied from the $HPC_CONTAVECT_CONF
    3 KB (309 words) - 20:40, 10 June 2022
  • GCE
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...e size, genomic repeat content and the heterozygsis rate of the sequencing sample, developed by Binghang Liu binghang.liu@qq.com). The estimated result can
    3 KB (311 words) - 18:57, 12 August 2022
  • Apptests
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> 1) Copy sample test script from /data/apps/test/apptests/run.sh into
    3 KB (331 words) - 20:52, 1 November 2023
  • BayesTraits
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...alyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and s
    3 KB (329 words) - 17:49, 26 August 2022
  • BAM-matcher
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...or determining whether two BAM files contain reads sequenced from the same sample or patient by counting genotype matches at common SNPs.
    3 KB (324 words) - 21:07, 6 December 2019
  • VarDictJava
    |{{#vardefine:batch|}} <!--SLURM SCRIPTS--> ...inal Perl VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel features s
    3 KB (334 words) - 17:23, 22 August 2022
  • Crossmapper
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...rate of read crossmapping when two or more organisms are sequenced as one sample. The software can be used for planning such kind of experimental setups as
    3 KB (326 words) - 17:40, 31 January 2022
  • BatMeth2
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> html report is generated about statistics of the sample.
    3 KB (324 words) - 18:57, 17 September 2021
  • MuSE
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...sue at each genomic locus. To improve overall accuracy, we further adopt a sample-specific error model to identify cutoffs, reflecting the variation in tumor
    3 KB (333 words) - 13:23, 19 July 2021
  • ClonalFrame
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> sample, while also estimating the chromosomal position of homologous
    3 KB (349 words) - 18:33, 12 August 2022
  • TGICL
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> * Sample run
    3 KB (340 words) - 20:47, 12 August 2022
  • FastQC
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...nly that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.
    3 KB (382 words) - 15:25, 15 August 2022
  • OpenCL
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> The following example shows how to build a sample code with OpenCL.
    3 KB (365 words) - 17:52, 19 August 2022
  • SHARCGS
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> * HPC_{{uc:{{#var:app}}}}_DATA - Sample data directory
    3 KB (313 words) - 22:42, 21 August 2022
  • Sabre
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...sequencing can currently produce hundreds of millions of reads per lane of sample and that number increases at a dizzying rate. Barcoding individual sequence
    3 KB (356 words) - 16:32, 2 November 2020
  • QualiMap
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> <!--PBS scripts-->
    3 KB (326 words) - 19:32, 24 August 2022
  • SourceTracker2
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...bs, since there is a 1 sink per job limit. Said another way, a single sink sample cannot be split up into multiple jobs.
    3 KB (357 words) - 14:19, 14 September 2020
  • Ngstools
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->
    5 KB (708 words) - 15:31, 14 December 2022
  • ANGSD
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...dium depth data. The software is written in C++ and has been used on large sample sizes.
    3 KB (355 words) - 12:42, 12 August 2022
  • VTC
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...development but currently performs association analyses on single or multi-sample VCFs and will print out detailed VCF summaries.
    3 KB (364 words) - 20:55, 12 August 2022
  • MONAI label
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> Load Next Sample
    3 KB (377 words) - 11:56, 19 August 2022
  • AtomEye
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> <!--PBS scripts-->
    3 KB (351 words) - 15:21, 12 August 2022
  • MotionCor2
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution br
    3 KB (375 words) - 20:33, 24 August 2022
  • Clara
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> The sample work flow for using MONAI is available at: https://github.com/zephyrie/mona
    3 KB (362 words) - 13:39, 15 August 2022
  • Deepvariant
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->
    3 KB (356 words) - 13:17, 16 April 2024
  • Bayenv
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...aphic regions. However, such comparisons are complicated by differences in sample sizes and the neutral correlation of allele frequencies across populations
    3 KB (388 words) - 19:03, 10 June 2022
  • New user training
    # [[Sample SLURM Scripts|SLURM Scheduler]] * [[Sample SLURM Scripts|SLURM Scheduler Sample Scripts]]
    16 KB (2,450 words) - 15:00, 14 August 2023
  • ProbABEL
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> * HPC_{{uc:{{#var:app}}}}_CONF - sample config file directory
    3 KB (371 words) - 19:35, 21 August 2022
  • METAL
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...test statistics and standard errors or (b) p-values across studies (taking sample size and direction of effect into account). METAL analysis is a convenient
    3 KB (426 words) - 19:27, 18 August 2022
  • Ngscheckmate
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...r the alignment and variant calling steps, respectively, to ensure correct sample annotation before further downstream analysis. Currently, it works only for
    3 KB (390 words) - 18:12, 27 May 2022
  • Themisto
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> A metanenomic sample is a set of sequences of reads from microbial life living in a particular e
    3 KB (401 words) - 20:57, 3 June 2022
  • UShER
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->
    3 KB (425 words) - 21:08, 13 January 2022
  • MZMine
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...based on the total amount of requested memory within a job. Pleas see the sample script below. Note that it appears to be necessary to simulate a virtual X1
    3 KB (417 words) - 13:28, 7 July 2023
  • Illumiprocessor
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...les (i.e., that you have merged mulitple files for each read from the same sample by combining fastq.gz files).
    4 KB (452 words) - 18:44, 15 August 2022
  • TWINSCAN
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> See the sample nscandriver.config at /apps/twinscan/4.1.2/conf/nscandriver.config for deta
    3 KB (386 words) - 20:20, 27 May 2022
  • RELION
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...run into this problem a simple fix to get the initial startup is to copy a sample project file from /apps/relion/conf/default_pipeline.star to the current wo
    3 KB (434 words) - 21:42, 21 August 2022
  • Chewiesnake
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> * Allele distances are hierarchically clustered and for each sample a cluster address as well as a unique (hashed) sequenced ID is provided.
    4 KB (457 words) - 15:02, 23 October 2023
  • Velvet
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> ...elvetg_MAX99 (using a max kmer of 99). There are also multiple contributed scripts available in the same location as the velvet binaries.
    4 KB (523 words) - 17:06, 14 December 2022
  • Lazypipe
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...ing of NGS libraries has been developed as a collection of C++, Perl and R scripts.
    4 KB (507 words) - 16:54, 14 December 2022
  • Fastsimcoal
    |{{#vardefine:job|}} <!--JOB SCRIPTS--> ...growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations.
    4 KB (481 words) - 15:25, 15 August 2022
  • BUSCO
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> busco -f -in target.fa -o SAMPLE -l ${HPC_BUSCO_DAT}/metazoa -m genome
    5 KB (607 words) - 19:38, 27 March 2023
  • HPG Scheduling
    ...bs. Users can create SLURM job scripts to submit jobs to the system. These scripts can, and should, be modified in order to control several aspects of your jo * See the [[Sample SLURM Scripts]] for several SLURM job script examples
    4 KB (656 words) - 18:36, 9 February 2024
  • SLURM Commands
    See also: [[Sample SLURM Scripts]]
    4 KB (574 words) - 15:30, 25 April 2024
  • Parabricks
    |{{#vardefine:job|1}} <!--JOB SCRIPTS--> <!--Job Scripts-->
    4 KB (574 words) - 21:25, 14 December 2022
  • Sample SLURM Scripts
    .../, and can be copied from there. If you choose to copy one of these sample scripts, please make sure you understand what each <code>#SBATCH</code> directive b ...or communication between jobs, view [[Multi-Threaded & Message Passing Job Scripts]]
    11 KB (1,685 words) - 14:21, 4 October 2023
  • QIIME
    |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> See the single-threaded and multi-threaded examples on the [[Sample SLURM Scripts]] page for more details.
    4 KB (555 words) - 15:15, 19 August 2022
  • HPG Computation
    ...o run computational analyses is through writing [[Sample SLURM Scripts|job scripts]] and sending them to the [[SLURM_Commands|scheduler]] to run. Some interfa * '''Only run workloads on compute nodes.''' Do not run scripts or applications on the login nodes beyond a [[Development_and_Testing#Login
    5 KB (760 words) - 17:35, 22 April 2024
  • MetaBCC-LR
    |{{#vardefine:job|1}} <!--JOB SCRIPTS--> <!--Job Scripts-->
    6 KB (774 words) - 14:28, 15 December 2022
  • R
    See the single-threaded and multi-threaded examples on the [[Sample SLURM Scripts]] page for more details.
    6 KB (981 words) - 20:45, 16 October 2023

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