CRAMINO

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

Installation

Download binaries from releases

With cargo

cargo install cramino

Usage

```bash cramino [OPTIONS]

ARGS: cram or bam file to check

OPTIONS: -t, --threads Number of parallel decompression threads to use [default: 4] --hist If histograms have to be generated --checksum If a checksum has to be calculated -h, --help Print help information -V, --version Print version information ```

Example output

text 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
• calculating a normalised number of reads per chromosome, e.g. to determine the sex or aneuploidies (--karyotype)
• histograms of read lengths and read identities, as below. (--hist)

text 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 ]: