enviro-lab
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ncbi-submit
ncbi-submit PublicA tool to prepare files and run/monitor programmatic submissions to NCBI
Python 4
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benchmark-deconvolute
benchmark-deconvolute PublicBenchmark Dataset Evaluation & COmparison of Nifty, Versatile, Objective Lineage-Unscrambling-Tool Execution
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hpc-interact
hpc-interact PublicUseful for scripting file transfer (sftp) and sending commands (ssh) to hpc - a wrapper for `expect`
Python 1
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covid-analysis
covid-analysis PublicSARS-CoV-2 sequencing and strain identification pipeline for nanopore samples
Nextflow
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freyja-plot
freyja-plot PublicPlotting lineage abundance for individual samples from aggregated freyja demix results
HTML
Repositories
- rereference Public
A tool for repositioning reads in a bam file relative to a different reference sequence. This is great if you want to align a SARS-CoV-2 sample to one of the more recent lineages and then reposition the coordinated to match the positions where the reads would map to the original Wuhan-Hu-1 reference sequence.
enviro-lab/rereference’s past year of commit activity - freyja-plot Public
Plotting lineage abundance for individual samples from aggregated freyja demix results
enviro-lab/freyja-plot’s past year of commit activity - benchmark-deconvolute Public
Benchmark Dataset Evaluation & COmparison of Nifty, Versatile, Objective Lineage-Unscrambling-Tool Execution
enviro-lab/benchmark-deconvolute’s past year of commit activity - hpc-interact Public
Useful for scripting file transfer (sftp) and sending commands (ssh) to hpc - a wrapper for `expect`
enviro-lab/hpc-interact’s past year of commit activity
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