CHM13
The complete sequence of a human genome (by marbl)
bowtie2
A fast and sensitive gapped read aligner (by BenLangmead)
| CHM13 | bowtie2 | |
|---|---|---|
| 13 | 2 | |
| 868 | 625 | |
| 2.0% | - | |
| 4.9 | 7.4 | |
| about 2 months ago | 5 days ago | |
| C++ | ||
| GNU General Public License v3.0 or later | 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.
CHM13
Posts with mentions or reviews of CHM13.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-09-14.
- VCF file for practice
-
NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).
- The human Y chromosome has been sequenced
- The human genome is, at long last, complete
-
The complete sequence of a human genome
Code https://github.com/marbl/CHM13
- Scientists publish the first complete human genome
-
The first fully complete human genome with no gaps is now available to view for scientists and the public, marking a huge moment for human genetics. The six papers are all published in the journal Science.
Liftover files are already available from https://github.com/marbl/CHM13
- Why there is a lot of Ns at the begining of the fasta file of all Human chromosomes
-
The Entire Human Genome Has Been Sequenced
If you’re serious, you can download the current fasta file from this page.
-
Digital Karyogram Derived From The Telomere-to-Telomere Consortium's CHM13/v1.1 Genome Assembly [OC]
I have created a simulated karyogram based on REPAVER visualisations of the Telomere-to-telomere Consortium's CHM13 assembly:
bowtie2
Posts with mentions or reviews of bowtie2.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-09-14.
-
NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).
- Computationally intensive steps in RNA-seq analysis
What are some alternatives?
When comparing CHM13 and bowtie2 you can also consider the following projects:
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
STAR - RNA-seq aligner
bwa-mem2 - The next version of bwa-mem
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
seq - A high-performance, Pythonic language for bioinformatics
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites
kraken2 - The second version of the Kraken taxonomic sequence classification system
vg - tools for working with genome variation graphs