search

single-cell-genetics / cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data
Apache License 2.0
74 stars 11 forks source link

Run time estimation #3

Closed coh-racng closed 5 years ago

coh-racng commented 5 years ago

How long would it approximately take to run cellSNP (Mode 1 with region_vcf) on HiSeq data with ~200M reads and 4000 cells? Do you have some examples of cellSNP runtimes for some number of cells, number of reads, and number of subprocesses (-p option)?

huangyh09 commented 5 years ago

Hi, I would expect less than 20 hours with around 20 CPUs for genotyping ~10M candiate SNPs in your case. The running time is roughly linear to the number of reads and the candidate SNPs.

We may have a guideline in near future. Thanks.