Galaxy | Europe | Accessible Workflow | Testing chloroplast assembly novoplasty

Testing chloroplast assembly novoplasty

Annotation:

Step	Annotation
Step 1: Input dataset SRR1328237_1.fasta.gz select at runtime
Step 2: Input dataset SRR1328237_2.fasta.gz select at runtime
Step 3: Input dataset Seed_RUBP.fasta select at runtime
Step 4: NOVOplasty Select read file type Separate reads Select file with forward reads Output dataset 'output' from step 1 Select file with reverse reads Output dataset 'output' from step 2 Select file with seed sequence Output dataset 'output' from step 3 Select reference file select at runtime Select platform Illumina Select mode None Select assembly type Chloroplast assembly (chloro) Set lower limit for the expected genome size range 120000 Set upper limit for the expected genome size range 200000 Set read length 151 Set total insert size of your paired end reads 450 Select read type Paired Extend seeds instead of finding matching reads False Set length of overlap between matching reads 39 Retain original IDs when saving assemled reads? False Finetune your insert size automatically? True Take quality scores into account? False Select output file(s) Assembled reads Contigs Circularized assembly Contig combinations Contigs Tmp Merged contigs Uncircularized assemblies Variance Heteroplasmy Heteroplasmy assemblies Linkage table heteroplasmy Possible NUMTs Possible NUMTs assemblies Linkage table NUMTs Circos mutations Circos links Config file Extended log Log

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ollie_white

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