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Fixed theiacov documentation to specify assembly order (#652)
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Michal-Babins authored Oct 17, 2024
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2 changes: 1 addition & 1 deletion docs/workflows/genomic_characterization/theiacov.md
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Expand Up @@ -959,7 +959,7 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
| aligned_bam | File | Primer-trimmed BAM file; generated during consensus assembly process | CL, ONT, PE, SE |
| artic_docker | String | Docker image utilized for read trimming and consensus genome assembly | CL, ONT |
| artic_version | String | Version of the Artic software utilized for read trimming and conesnsus genome assembly | CL, ONT |
| assembly_fasta | File | Consensus genome assembly; for lower quality flu samples, the output may state "Assembly could not be generated" when there is too little and/or too low quality data for IRMA to produce an assembly. Contigs will be ordered from smallest to largest when IRMA is used. | CL, ONT, PE, SE |
| assembly_fasta | File | Consensus genome assembly; for lower quality flu samples, the output may state "Assembly could not be generated" when there is too little and/or too low quality data for IRMA to produce an assembly. Contigs will be ordered from largest to smallest when IRMA is used. | CL, ONT, PE, SE |
| assembly_length_unambiguous | Int | Number of unambiguous basecalls within the consensus assembly | CL, FASTA, ONT, PE, SE |
| assembly_mean_coverage | Float | Mean sequencing depth throughout the consensus assembly. Generated after performing primer trimming and calculated using the SAMtools coverage command | CL, ONT, PE, SE |
| assembly_method | String | Method employed to generate consensus assembly | CL, FASTA, ONT, PE, SE |
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