Opis

Dorado je visokoučinkovit, jednostavan za korištenje ,pozivatelj baza za čitanje Oxford Nanopore.


Dostupne verzije:

VerzijaModulSupekPadobran
0.6.0scientific/dorado/0.6.0(tick) (error) 


Službena dokumentacija

Primjer korištenja

dorado-gpu.pbs
#!/bin/bash

#PBS -N dorado-run-gpu
#PBS -l select=1:ngpus=1
#PBS -q gpu

cd $PBS_O_WORKDIR

module load scientific/dorado/0.6.0

dorado basecaller $MOD/dna_r9.4.1_e8_hac@v3.3 test/ > test.bam

cuda:all

Dorado ima zadanu opciju cuda:all za sve vidljive grafičke procesore, sa ngpus ograničavamo taj broj. 


models

Dorado ima opciju automatski prepoznati modelkoji je potreban, skinuti ga i izbrisati nakon upotreben,no čvorovi nemaju pristup interentu, ta opcija nije moguća.

dorado-cpu.pbs
#!/bin/bash

#PBS -N dorado-run-cpu
#PBS -l select=1:ncpus=20:mem=200GB
#PBS -q cpu

cd $PBS_O_WORKDIR

module load scientific/dorado/0.6.0

dorado basecaller $MOD/dna_r9.4.1_e8_hac@v3.3 test/ -x "cpu" > test.bam

cpu

Sa opcijom -x "cpu" Doradu zadamo da koristi obične procesore, znantno je sporije izvođenje posla u odnosu sa grafičkim procesorima i koristi puno radne memorije.



  • dostupni modeli se nalaze pod $MOD varijablom: 

    • dna_r10.4.1_e8.2_260bps_fast@v3.5.2

    • dna_r10.4.1_e8.2_260bps_fast@v3.5.2_5mCG@v2

    • dna_r10.4.1_e8.2_260bps_fast@v4.0.0

    • dna_r10.4.1_e8.2_260bps_fast@v4.0.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_260bps_fast@v4.1.0

    • dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_260bps_hac@v3.5.2

    • dna_r10.4.1_e8.2_260bps_hac@v3.5.2_5mCG@v2

    • dna_r10.4.1_e8.2_260bps_hac@v4.0.0

    • dna_r10.4.1_e8.2_260bps_hac@v4.0.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_260bps_hac@v4.1.0

    • dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_260bps_sup@v3.5.2

    • dna_r10.4.1_e8.2_260bps_sup@v3.5.2_5mCG@v2

    • dna_r10.4.1_e8.2_260bps_sup@v4.0.0

    • dna_r10.4.1_e8.2_260bps_sup@v4.0.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_260bps_sup@v4.1.0

    • dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_fast@v3.5.2

    • dna_r10.4.1_e8.2_400bps_fast@v3.5.2_5mCG@v2

    • dna_r10.4.1_e8.2_400bps_fast@v4.0.0

    • dna_r10.4.1_e8.2_400bps_fast@v4.0.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_fast@v4.1.0

    • dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_fast@v4.2.0

    • dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_fast@v4.3.0

    • dna_r10.4.1_e8.2_400bps_hac@v3.5.2

    • dna_r10.4.1_e8.2_400bps_hac@v3.5.2_5mCG@v2

    • dna_r10.4.1_e8.2_400bps_hac@v4.0.0

    • dna_r10.4.1_e8.2_400bps_hac@v4.0.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_hac@v4.1.0

    • dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_hac@v4.2.0

    • dna_r10.4.1_e8.2_400bps_hac@v4.2.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_hac@v4.3.0

    • dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1

    • dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1

    • dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v1

    • dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2

    • dna_r10.4.1_e8.2_400bps_sup@v3.5.2

    • dna_r10.4.1_e8.2_400bps_sup@v3.5.2_5mCG@v2

    • dna_r10.4.1_e8.2_400bps_sup@v4.0.0

    • dna_r10.4.1_e8.2_400bps_sup@v4.0.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_sup@v4.1.0

    • dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_sup@v4.2.0

    • dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC_5hmC@v1

    • dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v2

    • dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v3.1

    • dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC@v2

    • dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v2

    • dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v3

    • dna_r10.4.1_e8.2_400bps_sup@v4.3.0

    • dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1

    • dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1

    • dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v1

    • dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2

    • dna_r10.4.1_e8.2_4khz_stereo@v1.1

    • dna_r10.4.1_e8.2_5khz_stereo@v1.1

    • dna_r10.4.1_e8.2_5khz_stereo@v1.2

    • dna_r9.4.1_e8_fast@v3.4

    • dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0

    • dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1

    • dna_r9.4.1_e8_hac@v3.3

    • dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0

    • dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1

    • dna_r9.4.1_e8_sup@v3.3

    • dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0

    • dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1

    • dna_r9.4.1_e8_sup@v3.6

    • rna002_70bps_fast@v3

    • rna002_70bps_hac@v3

    • rna004_130bps_fast@v3.0.1

    • rna004_130bps_hac@v3.0.1

    • rna004_130bps_sup@v3.0.1

    • rna004_130bps_sup@v3.0.1_m6A_DRACH@v1



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