CheckM - Quality assessment tool for the microbial genomes

Property Value
Distribution FreeBSD 12
Repository FreeBSD Ports Latest amd64
Package filename CheckM-1.0.18.txz
Package name CheckM
Package version 1.0.18
Package release -
Package architecture amd64
Package type txz
Category biology python
License GPLv3
Download size 197.57 KB
Installed size 1.23 MB
CheckM provides a set of tools for assessing the quality of genomes recovered
from isolates, single cells, or metagenomes. It provides robust estimates of
genome completeness and contamination by using collocated sets of genes that
are ubiquitous and single-copy within a phylogenetic lineage. Assessment of
genome quality can also be examined using plots depicting key genomic
characteristics (e.g., GC, coding density) which highlight sequences outside
the expected distributions of a typical genome. CheckM also provides tools for
identifying genome bins that are likely candidates for merging based on marker
set compatibility, similarity in genomic characteristics, and proximity within
a reference genome tree.


Package Version Architecture Repository
CheckM-1.0.18.txz 1.0.18 i386 FreeBSD Ports Latest
CheckM-1.0.18.txz 1.0.18 i386 FreeBSD Ports Quarterly
CheckM-1.0.18.txz 1.0.18 amd64 FreeBSD Ports Quarterly
CheckM - - -


Name Value
py36-DendroPy = 4.4.0
py36-matplotlib = 2.2.4_1
py36-numpy = 1.16.4_1,1
py36-pysam = 0.15.2
py36-scipy = 1.2.2_1
py36-setuptools = 41.1.0
python36 = 3.6.9


Type URL
Binary Package CheckM-1.0.18.txz
Source Package biology/checkm

Install Howto

Install CheckM txz package:

# pkg install CheckM

See Also

Package Description
ChipmunkPhysics-7.0.1_2.txz 2D physics engine written in C
Clp-1.16.10_8.txz Linear Programming Solver
Cockatrice-2.7.2.txz Virtual tabletop client and server for multiplayer card games
Coin-3.1.3_12.txz C++ 3D graphics library based on the Open Inventor 2.1 API
CoinMP-1.8.4_2.txz Optimization library with support for COIN-OR CLP, CBC, and CGL
CombBLAS-1.6.2_4.txz Combinatorial BLAS library: an extensible parallel graph library
CsoundQt-0.9.5_3.txz Csound frontend with editor, integrated help, widgets, other features
CuraEngine-15.04_5.txz Engine of slicing solution for RepRap 3D printers
DFileServer-1.1.3_1.txz Compact webserver designed to make sharing files easy
DRAWxtl-5.5.txz Crystal structure visualization tool
DoulosSIL-4.112_2.txz Doulos SIL TrueType font collection
DoulosSILCompact-4.110_3.txz Doulos SIL TrueType font collection, compact variant
Drawpile-2.1.13.txz Collaborative drawing program
E-Run-1.2_14.txz Simple epplet for launching arbitrary programs
FAudio-19.11.txz Accuracy-focused XAudio reimplementation