spades
bwa
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| spades | bwa | |
|---|---|---|
| 4 | 3 | |
| 660 | 1,453 | |
| 2.6% | - | |
| 9.3 | 2.7 | |
| 11 days ago | 13 days ago | |
| C++ | C | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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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.
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
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
What are some alternatives?
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
foldseek - Foldseek enables fast and sensitive comparisons of large structure sets.
mag - Assembly and binning of metagenomes
slivar - genetic variant expressions, annotation, and filtering for great good.
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
sra-tools - SRA Tools
sage - Proteomics search & quantification so fast that it feels like magic
bowtie - An ultrafast memory-efficient short read aligner
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
libBigWig - A C library for handling bigWig files