Opis
Dorado je visokoučinkovit, jednostavan za korištenje ,pozivatelj baza za čitanje Oxford Nanopore.
Dostupne verzije:
| Verzija | Modul | Supek | Padobran |
|---|---|---|---|
| 0.6.0 | scientific/dorado/0.6.0 |  |  |
Službena dokumentacija
Primjer korištenja
#!/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.
#!/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