bam2cram's Introduction

BAM file compression benchmark pipeline

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.

Rationale

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

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)

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