pysradb VS ariba

Compare pysradb vs ariba and see what are their differences.

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO (by saketkc)
Bioinformatics ncbi-sra ncbi-sra-archive sratoolkit bioinformatics-pipeline sra ena
Source Code
saketkc.github.io
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ariba

Antimicrobial Resistance Identification By Assembly (by sanger-pathogens)
Genomics sequencing next-generation-sequencing Research Bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Source Code
sanger-pathogens.github.io
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pysradb ariba
1 1
297 155
- 2.6%
7.3 3.0
8 months ago 8 months ago
Python Python
BSD 3-clause "New" or "Revised" License GNU General Public License v3.0 or later
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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pysradb

Posts with mentions or reviews of pysradb. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-10-05.
  • Systematic way to collect GEO datasets
    2 projects | /r/bioinformatics | 5 Oct 2022
    If you are okay with looking at already processed data, chdck out https://dee2.io/. Otherwise there is https://github.com/ncbi/sra-tools for getting fastq files (a cli tool) or https://github.com/saketkc/pysradb (python)

ariba

Posts with mentions or reviews of ariba. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-03-25.

What are some alternatives?

When comparing pysradb and ariba you can also consider the following projects:

sra-tools - SRA Tools

abricate - :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

kingfisher-download - Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

galaxy - Data intensive science for everyone.

GermlineMutationCalling - An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files

MGEfinder - A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

edgecase - A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

abritamr - A pipeline for running AMRfinderPlus and collating results into functional classes

16SMaRT - 16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).

hgvs - Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

pysradb vs sra-tools ariba vs abricate pysradb vs kingfisher-download ariba vs galaxy pysradb vs GermlineMutationCalling ariba vs MGEfinder pysradb vs edgecase ariba vs abritamr ariba vs edgecase ariba vs 16SMaRT ariba vs hgvs ariba vs deepvariant