viralrecon.md formated

bu_isciii/assets/reports/results/viralrecon.md

@@ -1,70 +1,70 @@
-## Viralrecon
+# Viralrecon
 
 Here we describe the results from the Viralrecon pipeline for viral genome reconstruction.
 
 > [!WARNING]
 > Some of the files listed here may not be in your  `RESULTS` folder. It will depend on the analysis you requested.
 
-### Mapping approach results
+## Mapping approach results
 
 * mapping_illumina.xlsx: statistics for mapped reads against viral and host genomes.
-  - run: Run name
-  - user: User name
-  - host: Host name
-  - Virussequence: Reference virus used
-  - sample: Sample name
-  - totalreads: Total reads after trimming
-  - readshostR1: Total reads of host genome in R1
-  - readshost: Total reads of host genome in R1 and R2
-  - %readshost: Percentage of reads that correspond to the host genome
-  - readsvirus: Number of reference viral genome reads
-  - %readsvirus: Percentage of reference viral genome reads
-  - unmappedreads: number of reads that did not correspond to viral reference or host genome.
-  - %unmapedreads: Percentage of reads that did not correspond to viral reference or host genome.
-  - medianDPcoveragevirus: Median depth of coverage of the reference viral genome
-  - Coverage>10x(%): Percentage of viral reference genome coverage to more than 10X
-  - Variantsinconsensusx10: Number of variants included in the consensus after filtering: more than 10X and 0.75 AF
-  - %Ns10x: Percentage of consesus genome masked due to having less than 10X depth
-  - Lineage: Pangolin assigned lineage. *Warning: Only for SARS-CoV-2 sequencing data*
-  - Date: Analysis date. *Warning: Only for SARS-CoV-2 sequencing data*
+  * run: Run name
+  * user: User name
+  * host: Host name
+  * Virussequence: Reference virus used
+  * sample: Sample name
+  * totalreads: Total reads after trimming
+  * readshostR1: Total reads of host genome in R1
+  * readshost: Total reads of host genome in R1 and R2
+  * %readshost: Percentage of reads that correspond to the host genome
+  * readsvirus: Number of reference viral genome reads
+  * %readsvirus: Percentage of reference viral genome reads
+  * unmappedreads: number of reads that did not correspond to viral reference or host genome.
+  * %unmapedreads: Percentage of reads that did not correspond to viral reference or host genome.
+  * medianDPcoveragevirus: Median depth of coverage of the reference viral genome
+  * Coverage>10x(%): Percentage of viral reference genome coverage to more than 10X
+  * Variantsinconsensusx10: Number of variants included in the consensus after filtering: more than 10X and 0.75 AF
+  * %Ns10x: Percentage of consesus genome masked due to having less than 10X depth
+  * Lineage: Pangolin assigned lineage. *Warning: Only for SARS-CoV-2 sequencing data*
+  * Date: Analysis date. *Warning: Only for SARS-CoV-2 sequencing data*
 * mapping_consensus: this folder contains the masked (<10x) genomes obtained with consensus sequences using mapping and majority variant calling
 * variants_annot: table with all annotated variants. *Warning: Only when annotation .gff file was provided*
 * variants_long_table.xlsx: Table with variants for all the samples in long format. *Warning: Only when annotation .gff file was provided*
-  - SAMPLE: sample name
-  - CHROM: Reference ID
-  - POS: Position of the variant
-  - REF: Ref allele
-  - ALT: Alt allele
-  - FILTER: Column indicating if the variant passed the filters. If PASS the variant passed all the filters. If not, the name of the filter that wasn't passed will appear
-  - DP: Position depth
-  - REF_DP: Ref allele depth
-  - ALT_DP: Alt allele depth
-  - AF: Allele frequency
-  - GENE: Gene name in annotation file​
-  - EFFECT: Effect of the variant
-  - HGVS_C: Position annotation at CDS level
-  - HGVS_P: Position annotation at protein level
-  - HGVS_P_1LETTER: Position annotation at protein level with the aminoacid annotation in 1 letter format
-  - Caller: Variant caller used
+  * SAMPLE: sample name
+  * CHROM: Reference ID
+  * POS: Position of the variant
+  * REF: Ref allele
+  * ALT: Alt allele
+  * FILTER: Column indicating if the variant passed the filters. If PASS the variant passed all the filters. If not, the name of the filter that wasn't passed will appear
+  * DP: Position depth
+  * REF_DP: Ref allele depth
+  * ALT_DP: Alt allele depth
+  * AF: Allele frequency
+  * GENE: Gene name in annotation file​
+  * EFFECT: Effect of the variant
+  * HGVS_C: Position annotation at CDS level
+  * HGVS_P: Position annotation at protein level
+  * HGVS_P_1LETTER: Position annotation at protein level with the aminoacid annotation in 1 letter format
+  * Caller: Variant caller used
 * pangolin.xlsx: Pangolin complete results *Warning: Only for SARS-CoV-2 sequencing data*
 * nextclade.xlsx: Results from Nextclade *Warning: Only for SARS-CoV-2 sequencing data*
 
-### *de novo* assembly approach results
+## *de novo* assembly approach results
 
 * assembly_stats.xlsx: Stats of the *de novo* assembly steps. This table contains the following columns:
-  - run: Run name
-  - user: User name
-  - host: Host name
-  - Virussequence: Reference virus used
-  - sample: Sample name
-  - totalreads: Total reads after trimming
-  - readshostR1: Total reads of host genome in R1
-  - readshost: Total reads of host genome in R1 and R2
-  - %readshost: Percentage of reads that correspond to the host genome
-  - Non-host-reedas: Number of reads remaining after host removal
-  - \#Contigs: Number of contigs in the assembly
-  - Largest contig: Size in nucleotides of the larges contig in the assembly
-  - % Genome fraction: Percentage of the reference genome covered by the assembly. *Warning: Only when reference genome was provided*
+  * run: Run name
+  * user: User name
+  * host: Host name
+  * Virussequence: Reference virus used
+  * sample: Sample name
+  * totalreads: Total reads after trimming
+  * readshostR1: Total reads of host genome in R1
+  * readshost: Total reads of host genome in R1 and R2
+  * %readshost: Percentage of reads that correspond to the host genome
+  * Non-host-reedas: Number of reads remaining after host removal
+  * \#Contigs: Number of contigs in the assembly
+  * Largest contig: Size in nucleotides of the larges contig in the assembly
+  * % Genome fraction: Percentage of the reference genome covered by the assembly. *Warning: Only when reference genome was provided*
 * assembly_spades: Scaffolds fasta files with the spades de novo assembly. *Warning: Only when NO reference genome was provided, or reference genome didn't match*
 * abacas_assembly: spades de novo assembly where contigs were contiguated using ABACAS and the reference genome. *Warning: Only when reference genome was provided*