bwa
spades
bwa | spades | |
---|---|---|
3 | 4 | |
1,453 | 664 | |
- | 1.7% | |
2.7 | 9.3 | |
18 days ago | 3 days ago | |
C | C++ | |
GNU General Public License v3.0 only | 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.
bwa
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my friend showed me his code, thees are all functions
Check out these sweet macros (from the same repo): https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/kbtree.h
- Scientists Are Finding Fungi in Cancerous Tumors
- Burrows–Wheeler Transform
spades
- my friend showed me his code, thees are all functions
- What are some good examples of well-engineered bioinformatics pipelines?
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Genome analysis cost
If you do DNA sequencing and receive the sequencing files as fastq files (normal from sequencing) then spades to assemble the genome, then put it through PROKKA to annotate it. Here's a beginners guide, the most difficult part is downloading the programs onto your laptop.
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Is it possible to assemble a complete bacterial genome using short reads?
MetaSpades has a cool option to hybrid reform contigs using short and long reads so you could pair short read data and long read data (PacBio/ONT) to get the best hybrid assembly with high throughput and long reference reads for resolving the reassembling. https://github.com/ablab/spades
What are some alternatives?
foldseek - Foldseek enables fast and sensitive comparisons of large structure sets.
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
slivar - genetic variant expressions, annotation, and filtering for great good.
mag - Assembly and binning of metagenomes
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
sra-tools - SRA Tools
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
bowtie - An ultrafast memory-efficient short read aligner
sage - Proteomics search & quantification so fast that it feels like magic
libBigWig - A C library for handling bigWig files
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.