spades
juicer
spades | juicer | |
---|---|---|
4 | 1 | |
664 | 390 | |
1.7% | 3.8% | |
9.3 | 0.0 | |
4 days ago | 3 months ago | |
C++ | Shell | |
GNU General Public License v3.0 or later | MIT License |
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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
juicer
What are some alternatives?
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
sage - Proteomics search & quantification so fast that it feels like magic
mag - Assembly and binning of metagenomes
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
smk-simple-slurm - A simple Snakemake profile for Slurm without --cluster-config