edgecase
A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference. (by LankyCyril)
pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO (by saketkc)
| edgecase | pysradb | |
|---|---|---|
| 1 | 1 | |
| 14 | 297 | |
| - | - | |
| 2.1 | 7.3 | |
| 4 months ago | 8 months ago | |
| Python | Python | |
| GNU General Public License v3.0 only | 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.
edgecase
Posts with mentions or reviews of edgecase.
We have used some of these posts to build our list of alternatives
and similar projects.
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Know a tool that visualizes read sequence extending beyond reference coordinates?
that said, just looking at the raw "show softclipped sequence" in e.g. igv may not be the best scenario either, so creating a custom visualization may be needed anyways. here is another tool i found https://github.com/lankycyril/edgecase from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8256856/
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.
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Systematic way to collect GEO datasets
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)
What are some alternatives?
When comparing edgecase and pysradb you can also consider the following projects:
ariba - Antimicrobial Resistance Identification By Assembly
sra-tools - SRA Tools
pipeline-structural-variation - Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
kingfisher-download - Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
GermlineMutationCalling - An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files