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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

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