spades
SPAdes Genome Assembler (by ablab)
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly (by trinityrnaseq)
spades | trinityrnaseq | |
---|---|---|
4 | 6 | |
664 | 803 | |
1.7% | 0.6% | |
9.3 | 2.8 | |
4 days ago | 18 days ago | |
C++ | Perl | |
GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" License |
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.
spades
Posts with mentions or reviews of spades.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-25.
- 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
trinityrnaseq
Posts with mentions or reviews of trinityrnaseq.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-05.
- What are some good examples of well-engineered bioinformatics pipelines?
-
Can I get so guidance on how to run sample data in trinityrnaseq-Trinity-v2.13.2 in Ubuntu Linux ?
The screen shot suggests you are not able to actually compile/install trinity. The cmake command is not used to run it. After you download and unpack the trinity software package: https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.13.2/trinityrnaseq-v2.13.2.FULL.tar.gz, you should look at the INSTALL file, which tells you to:
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Beginner question for using dockerized trinity
I'm trying commands from the Docker site and the trinity site. When I try to run the command, it behaves like the code is incomplete (hitting enter just gives me a new line). To my understanding, the issue can be either in the pathway/to/files part of the code, of in the trinityrnaseq/trinityrnaseq part.
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GATK version issue with variant calling following Trinity pipeline python script
For my analysis I am trying to do variant calling on my transcriptome. I am following the Trinity github pipeline for variant calling, in which they provided a python script for GATK for the variant calling. I use SLURM to run this job for me:
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What's your bioinformatics bible? Any bibliography recommendations for experimental design?
Since you're an R user, I would recommend Bioconductor. Here's an excellent tutorial on how to analyze RNA-seq data (make sure that you're R version is up to date!): https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html . However, if you want to assemble raw transcriptome data, then Trinity is a great tool (https://github.com/trinityrnaseq/trinityrnaseq/wiki).
- Can DESeq2 and edgeR be used on Trinity assembled transcripts given that only the longest isoforms are used?
What are some alternatives?
When comparing spades and trinityrnaseq you can also consider the following projects:
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
mag - Assembly and binning of metagenomes
sage - Proteomics search & quantification so fast that it feels like magic
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.