Opis

HERRO (Haplotype-aware ERRor Correction) vrlo je precizan, haplotip alat za duboko učenje za ispravljanje pogrešaka Nanopore R10.4.1, Kit 14 očitavanja (preporučuje se duljina od ≥ 10000 bp).


Dostupne verzije

VerzijaModulSupekPadobran
0.1.0scientific/herro/0.1.0(tick) (error) 


Službena dokumentacija


Primjer korištenja

1. herro-preprocess
#PBS -N herro_clean
#PBS -q cpu
#PBS -l select=1:ncpus=40:mem=80GB

cd $PBS_O_WORKDIR

module load scientific/herro/0.1.0

herro.sh preprocess.sh hg002v1.0.fastq hg002v1.0.out $NCPUS 5


2. herro-ids
#PBS -N herro_clean
#PBS -q cpu
#PBS -l select=1:ncpus=10:mem=20GB

cd $PBS_O_WORKDIR

module load scientific/herro/0.1.0

herro.sh seqkit seq -ni hg002v1.0.out.fastq.gz > hg002v1.0_ids
3. herro-create_batched_alignments
#PBS -N herro_clean
#PBS -q cpu
#PBS -l select=1:ncpus=40:mem=200GB

cd $PBS_O_WORKDIR

module load scientific/herro/0.1.0

herro.sh create_batched_alignments.sh hg002v1.0.out.fastq.gz hg002v1.0_ids $NCPUS batches
  • 2 modela su dostupna pod varijablom $MODELS
    • model_R9_v0.1.pt(eksperimentalni)
    • model_v0.1.pt
4. herro-inference
#!/bin/bash
#PBS -N herro_clean
#PBS -q gpu
#PBS -l select=1:ncpus=20:mem=120GB:ngpus=1

cd $PBS_O_WORKDIR

module load scientific/herro/0.1.0

herro.sh herro inference --read-alns batches/ -t $NCPUS -m $MODELS/model_v0.1.pt -b 64 hg002v1.0.out.fastq.gz hg002v1.error_corrected.fasta