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jaleezyy
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covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
MIT License
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Add FreeBayes variant calling and restore multiple pool sample support
#106
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jaleezyy
closed
3 years ago
jaleezyy
commented
3 years ago
Add FreeBayes consensus and variant calling in parallel with iVar (option can be activated in config file along with BreSeq)
Updates to SIGNAL postprocess to indicate differences in variant calls between iVar and FreeBayes
Restore multiple pool samples support (now only applies to samples sharing the same sample identifier in the sample table)
Updated sample table generator script (
generate_sample_table.sh
) to handle FASTQ files for multiple pool samples
Updates to ncov-tools submodule (automatically formats data for ncov-tools v1.4+, but manual run of ncov-tools is still required)
Updated README
generate_sample_table.sh) to handle FASTQ files for multiple pool samples