asleonard / cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

CRAMINO

A tool for quick quality assessment of cram and bam files, intended for long read sequencing.

Installation

Preferably, for most users, download a ready-to-use binary for your system to add directory on your $PATH from the releases.
You may have to change the file permissions to execute it with chmod +x cramino

Alternatively, use conda to install
conda install -c bioconda cramino

Or for Rust developers, build cramino with cargo:
cargo install cramino

Usage

cramino [OPTIONS] <INPUT>

ARGS:
    <INPUT>    cram or bam file to check (or - to read from stdin)

OPTIONS:
    -t, --threads <THREADS>            Number of parallel decompression threads to use [default: 4]
    -m, --min-read-len <MIN_READ_LEN>  Minimal length of read to be considered [default: 0]
    --hist                             If histograms have to be generated
    --checksum                         If a checksum has to be calculated
    --arrow <ARROW>                    Write data to a feather format
    --karyotype                        Provide normalized number of reads per chromosome
    --phased                           Calculate metrics for phased reads
    --spliced                          Calculate metrics for spliced reads
    -h, --help                         Print help information
    -V, --version                      Print version information

Example output

File name       example.cram
Number of reads 14108020
Yield [Gb]      139.91
N50     17447
Median length   6743.00
Mean length     9917
Median identity 94.27
Mean identity   92.53
Path    alignment/example.cram
Creation time   09/09/2022 10:53:36

A 140Gbase bam file is processed in 12 minutes, using <1Gbyte of memory. Note that the identity score above is defined as the gap-compressed identity.

Optional output

• a checksum to check if files were updated/changed or corrupted. (--checksum)
• an arrow file for use within NanoPlot and NanoComp (--arrow <filename>)
• calculating a normalised number of reads per chromosome, e.g. to determine the sex or aneuploidies (--karyotype)
• information about the phase blocks. (--phased)
• histograms of read lengths and read identities, as below. (--hist)

 70.97195691947476 ..  71.97292392225151 [  122235 ]: ∎∎
 71.97292392225151 ..  72.97389092502823 [  136051 ]: ∎∎∎
 72.97389092502823 ..  73.97485792780498 [  145876 ]: ∎∎∎
 73.97485792780498 ..   74.9758249305817 [  157751 ]: ∎∎∎
  74.9758249305817 ..  75.97679193335844 [  179551 ]: ∎∎∎∎
 75.97679193335844 ..  76.97775893613516 [  171769 ]: ∎∎∎∎
 76.97775893613516 ..   77.9787259389119 [  159340 ]: ∎∎∎
  77.9787259389119 ..  78.97969294168863 [  151355 ]: ∎∎∎
 78.97969294168863 ..  79.98065994446536 [  146207 ]: ∎∎∎
 79.98065994446536 ..  80.98162694724209 [  142832 ]: ∎∎∎
 80.98162694724209 ..  81.98259395001882 [  140902 ]: ∎∎∎
 81.98259395001882 ..  82.98356095279556 [  143909 ]: ∎∎∎
 82.98356095279556 ..  83.98452795557229 [  149142 ]: ∎∎∎
 83.98452795557229 ..  84.98549495834902 [  158386 ]: ∎∎∎
 84.98549495834902 ..  85.98646196112576 [  176819 ]: ∎∎∎∎
 85.98646196112576 ..  86.98742896390249 [  199558 ]: ∎∎∎∎
 86.98742896390249 ..  87.98839596667922 [  234573 ]: ∎∎∎∎∎
 87.98839596667922 ..  88.98936296945595 [  280849 ]: ∎∎∎∎∎∎
 88.98936296945595 ..  89.99032997223267 [  348535 ]: ∎∎∎∎∎∎∎∎
 89.99032997223267 ..   90.9912969750094 [  445640 ]: ∎∎∎∎∎∎∎∎∎∎
  90.9912969750094 ..  91.99226397778614 [  583424 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎
 91.99226397778614 ..  92.99323098056287 [  776111 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
 92.99323098056287 ..   93.9941979833396 [ 1051370 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
  93.9941979833396 ..  94.99516498611634 [ 1414103 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
 94.99516498611634 ..  95.99613198889307 [ 1833438 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
 95.99613198889307 ..   96.9970989916698 [ 2084833 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
  96.9970989916698 ..  97.99806599444653 [ 1620179 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
 97.99806599444653 ..  98.99903299722327 [  416669 ]: ∎∎∎∎∎∎∎∎∎
 98.99903299722327 ..                100 [   39254 ]: