spades
prokka
spades | prokka | |
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4 | 5 | |
664 | 754 | |
1.7% | - | |
9.3 | 0.0 | |
4 days ago | 24 days ago | |
C++ | Perl | |
GNU General Public License v3.0 or later | - |
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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
prokka
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orfs in DNA
If you need more accurate ORF(CDS) prediction including functional annotation, I recommend using CLI tools such as prokka, bakta, or DFAST (DFAST is also available in a web version).
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
reCOGnizer (https://github.com/iquasere/reCOGnizer) can annotate with COGs, and the other databases available at CDD. It obtains all information concerning COGs description and categories, and outputs krona plots and TSV tables in formats easy to analyze. There is also mantis (https://github.com/PedroMTQ/mantis), prokka (https://github.com/tseemann/prokka) and DFAST (https://github.com/nigyta/dfast_core), the latter two work on contigs and the first two are for proteins
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ORF prediction for non-model organism with DNA sequence only
I just checked out Prokka, which uses Prodigal to predict genes. They do not seem to have any reservations for viruses. Thus, I recommend using Prokka directly, since that will conveniently add functional annotations.
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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.
What are some alternatives?
mag - Assembly and binning of metagenomes
Prodigal - Prodigal Gene Prediction Software
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
dfast_core - DDBJ Fast Annotation and Submission Tool
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
BRAKER - BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
sage - Proteomics search & quantification so fast that it feels like magic
funannotate - Eukaryotic Genome Annotation Pipeline
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database