First test the pipeline with a dry run: `snakemake -np`. This will show you the steps and commands that will be executed. Check the commands and file names to see if there’s any mistake. If all looks ok, you can now run your pipeline
First test the pipeline with a dry run: `snakemake -np`. This will show you the steps and commands that will be executed. Check the commands and file names to see if there’s any mistake. If all looks ok, you can now run your pipeline
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@@ -109,14 +108,7 @@ The most important files are and directories are:
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@@ -109,14 +108,7 @@ The most important files are and directories are:
-**results** directory that contains
-**results** directory that contains
-**{prefix}_oneline.k32.w100.ntLink-arks.longstitch-scaffolds.fa.PolcaCorrected.fa** final assembly
-**{prefix}_oneline.k32.w100.ntLink-arks.longstitch-scaffolds.fa.PolcaCorrected.fa** final assembly
- assembly_stats_\<prefix>.txt file with assembly statistics for the final assembly
- assembly_stats_\<prefix>.txt file with assembly statistics for the final assembly
-**variant_calling** directory with variant calling VCF files with long and short reads, as well as VCF stats
- {prefix}_shortreads.vcf.gz
- {prefix}_shortreads.vcf.gz.stats
- {prefix}_longreads.vcf.gz
- {prefix}_longreads.vcf.gz.stats
Both the short reads and the long reads variant calling VCFs are filtered for `QUAL > 20`. Freebayes (short read var calling) is ran with parameters `--use-best-n-alleles 4 --min-base-quality 10 --min-alternate-fraction 0.2 --haplotype-length 0 --ploidy 2 --min-alternate-count 2`. For more details check the Snakefile.
-**genome_alignment** directory with results and figure from whole genome alignment
-**genome_alignment** directory with results and figure from whole genome alignment
- {prefix}_{species}.png
- {prefix}_{species}.png
-**mapped** directory that contains the bam file with long reads mapped to the new assembly
-**mapped** directory that contains the bam file with long reads mapped to the new assembly
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@@ -126,3 +118,5 @@ Both the short reads and the long reads variant calling VCFs are filtered for `Q
...
@@ -126,3 +118,5 @@ Both the short reads and the long reads variant calling VCFs are filtered for `Q