Command & Options:
samtools vs sambamba
- samtools
- sambamba
More information:

Sambamba can replace most of the functionality of samtools. The main advantage of sambamba over samtools was parallelized BAM reading and writing.

Command & Options:

sambamba-view, sambamba-sort, sambamba-index, sambamba-merge, sambamba-slice, sambamba-flagstat, sambamba-markdup

sambamba-view

tool for extracting information from SAM/BAM files

-S, --sam-input
    #Specify that the input is SAM file (default is BAM for all operations).
-l, --compression-level=COMPRESSION_LEVEL
    # Set compression level for BAM output, a number from 0 to 9.
-t, --nthreads=NTHREADS
    # Number of threads to use.
-s, --subsample=FRACTION
    # subsample reads (read pairs)
--subsampling-seed=SEED
    # set seed for subsampling to re-emerge the results.

sambamba-sort

sambamba sort does an external sort on input file.

-m, --memory-limit=LIMIT
    # Sets an upper bound for used memory. Default memory limit is 512MiB. suffix K/KiB/KB/M/MiB/MB/G/GiB/GB recognized.
-n, --sort-by-name
    # Default is 'coordinate'.

sambamba-index

sambamba index builds an index for a sorted by coordinate BAM file.

sambamba-markdup

sambamba-markdup - finding duplicate reads in BAM file

-r, --remove-duplicates
--hash-table-size=HASHTABLESIZE
# size of hash table for finding read pairs (default is 262144 reads); will be rounded down to the nearest power of two; should be > (average coverage) * (insert size) for good performance
--overflow-list-size=OVERFLOWLISTSIZE
# size of the overflow list where reads, thrown away from the hash table, get a second chance to meet their pairs (default is 200000 reads); increasing the size reduces the number of temporary files created

`samtools` vs `sambamba`

`samtools`

samtools sort -@ 4 -l 9 ~/SARS_CoV_2/bam/P3-VERO-P3-1-vero_L4.bam -o ~/SARS_CoV_2/vs/P3-VERO-P3-1-vero_L4_sort.bam

In this process, samtools sort created 208 Temporary files, taking 01:14:09.
sambamba - 图1

`sambamba`

sambamba sort -t 4 -l 9 ~/SARS_CoV_2/mapping/P3-VERO-P3-1-vero_L4.bam -o ~/SARS_CoV_2/vs/P3-VERO-P3-1-vero_L4_sort1.bam

sambamba sort did not create Temporary files, but took 01:51:46.
When sorting a BAM file, Sambamba is not quicker than Samtools single-threaded.

More information:

https://lomereiter.github.io/sambamba/docs/sambamba-view.html

sambamba