1 unstable release
0.9.0 | Oct 26, 2022 |
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#300 in Biology
25KB
525 lines
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
cramino [OPTIONS] <INPUT>
ARGS:
<INPUT> cram or bam file to check
OPTIONS:
-t, --threads <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
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
)
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 ]:
Dependencies
~22–34MB
~572K SLoC