amr
bwa-mem2
amr | bwa-mem2 | |
---|---|---|
1 | 2 | |
242 | 683 | |
5.0% | 1.9% | |
7.1 | 3.3 | |
12 days ago | 12 days ago | |
C++ | C++ | |
GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
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.
amr
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No antibiotic resistance genes in plasmidSPAdes assembly
https://github.com/ncbi/amr this tool will report the contig and coordinates for any AMR gene it detects in your assembly. If you want to know which genes are nearby you should also annotate your genome (with prokka for example) as the other response suggested
bwa-mem2
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Anyone use DRAGEN-GATK?
If you haven’t heard of it already you may want to check out https://github.com/bwa-mem2/bwa-mem2 which is a faster version of bwa-mem. I’ve been using it for a while now and found it to be quite stable, same results as the original and the speed improvement is nice.
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Software Development Project
I’ve recently switched to bwa mem2 and the speed increase is nice for what is basically a drop in replacement (after a bit of validation to make sure that was true). https://github.com/bwa-mem2/bwa-mem2
What are some alternatives?
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
bowtie2 - A fast and sensitive gapped read aligner
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
htslib - C library for high-throughput sequencing data formats
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
vg - tools for working with genome variation graphs
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
GenomicSQLite - Genomics Extension for SQLite
seqstats - Quick summary statistics on fasta/fastq(.gz) files
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites
Klib - A standalone and lightweight C library