trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly (by trinityrnaseq)
gatk4-genome-processing-pipeline-azure
Workflows used for processing whole genome sequence data + germline variant calling. (by microsoft)
trinityrnaseq | gatk4-genome-processing-pipeline-azure | |
---|---|---|
6 | 4 | |
803 | 7 | |
0.6% | - | |
2.8 | 0.0 | |
16 days ago | about 2 months ago | |
Perl | wdl | |
BSD 3-clause "New" or "Revised" License | 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.
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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.
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?
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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?
gatk4-genome-processing-pipeline-azure
Posts with mentions or reviews of gatk4-genome-processing-pipeline-azure.
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?
-
Do you know how to get CNVs out of WES data sorted.bam files? (Free)
The GATK suite is pretty standard for calling germline mutations. Somatic mutation calling is a lot newer/trickier, so I'm just going to link to the GDC's practices.
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Best way to document tool?
This pre-processing pipeline from Microsoft (adapted from the Broad Institute/GATK) is pretty well-documented - at least in my opinion - with input requirements, expected outputs, software requirements, etc.
What are some alternatives?
When comparing trinityrnaseq and gatk4-genome-processing-pipeline-azure you can also consider the following projects:
spades - SPAdes Genome Assembler
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
sage - Proteomics search & quantification so fast that it feels like magic
veba - A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
trinityrnaseq vs spades
gatk4-genome-processing-pipeline-azure vs juicer
trinityrnaseq vs rnaseq
gatk4-genome-processing-pipeline-azure vs sv-callers
trinityrnaseq vs sage
gatk4-genome-processing-pipeline-azure vs sage
trinityrnaseq vs juicer
gatk4-genome-processing-pipeline-azure vs veba
gatk4-genome-processing-pipeline-azure vs rnaseq
gatk4-genome-processing-pipeline-azure vs seqkit
gatk4-genome-processing-pipeline-azure vs spades