From 6d8fd1736244e1e233da8f417a3dd1b092f377a1 Mon Sep 17 00:00:00 2001 From: Michal Babinski Date: Thu, 17 Oct 2024 15:29:31 -0400 Subject: [PATCH] Fixed theiacov documentation to specify assembly order (#652) --- docs/workflows/genomic_characterization/theiacov.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflows/genomic_characterization/theiacov.md b/docs/workflows/genomic_characterization/theiacov.md index f877ba540..a97f85246 100644 --- a/docs/workflows/genomic_characterization/theiacov.md +++ b/docs/workflows/genomic_characterization/theiacov.md @@ -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 |