Benchmarks of CRAM 2.1 and 3.0 are using the faster CRAM codecs; primarily deflate and rANS.
Also included is the performance of the proposed CRAM v3.1 standard. This is not yet a ratified GA4GH standard, but these figures give indicative results.
The following Samtools (version 1.14) profiles are tested:
| Profile | CRAM versions | options |
|---|---|---|
| default | 3.0, 3.1 | |
| fast | 3.0, 3.1 | seqs_per_slice=1000, level=1 |
| normal | 3.0, 3.1 | seqs_per_slice=10000 |
| small | 3.0 | seqs_per_slice=25000, level=6,use_bzip2 |
| small | 3.1 | seqs_per_slice=25000, level=6,use_bzip2,use_fqz |
| archive | 3.0 | seqs_per_slice=100000,level=7,use_bzip2 |
| archive | 3.1 | seqs_per_slice=100000,level=7,use_bzip2,use_fqz,use_arith |
| archive lzma | 3.0 | seqs_per_slice=100000,level=7,use_bzip2, use_lzma |
| archive lzma | 3.1 | seqs_per_slice=100000,level=7,use_bzip2,use_fqz,use_arith, use_lzma |
Requirements This workflow requires at least 2 CPUs and 4GB of memory.
Usage:
nextflow run main.nf --input input.csv --reference reference.fasta [Options]
Inputs Options:
--input Input csv file with sample_id, bam and bai paths
--reference Reference fasta file
Resource Options:
--cpus Number of CPUs (int)
(default: 2)
--max_cpus Maximum number of CPUs (int)
(default: 2)
--memory Memory (memory unit)
(default: 4 GB)
--max_memory Maximum memory (memory unit)
(default: 4 GB)
--time Time limit (time unit)
(default: 8h)
--max_time Maximum time (time unit)
(default: 8h)