ngsLD
Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework (by fgvieira)
ngsLD | NgsRelate | |
---|---|---|
1 | 1 | |
38 | 39 | |
- | - | |
4.9 | 4.5 | |
7 months ago | 6 months ago | |
C++ | C++ | |
GNU General Public License v3.0 only | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
ngsLD
Posts with mentions or reviews of ngsLD.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-19.
-
angsd file conversion + subsetting help?
However, I realised I needed to go back and run NGSrelate on my samples (oops). This requires DoGlf 3, which according to the documentation, and this link, is a binary beagle file. I was in the process of rerunning angsd when my CPU hours ran out on the server, and it crashed (lets call this angsd run 2). It has however finished 4 days worth of analyses that I don't want to have to rerun.
NgsRelate
Posts with mentions or reviews of NgsRelate.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-19.
-
angsd file conversion + subsetting help?
However, I realised I needed to go back and run NGSrelate on my samples (oops). This requires DoGlf 3, which according to the documentation, and this link, is a binary beagle file. I was in the process of rerunning angsd when my CPU hours ran out on the server, and it crashed (lets call this angsd run 2). It has however finished 4 days worth of analyses that I don't want to have to rerun.
What are some alternatives?
When comparing ngsLD and NgsRelate you can also consider the following projects:
glactools - command-line tools for the management of genotype likelihoods and allele counts
TPMCalculator - TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
pypop - PyPop: Python for Population Genomics
chaotix - The chaotix operating system! (Previously known as Magma or Psychix)