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• 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

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