Galaxy | Published Workflow | Assembling the S. aureus genome using SOAPdenovo2

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Published Workflows | peterli | Assembling the S. aureus genome using SOAPdenovo2

Galaxy Workflow ' Assembling the S. aureus genome using SOAPdenovo2'

Step	Annotation
Step 1: Input dataset Input Dataset select at runtime	frag_1.fastq
Step 2: Input dataset Input Dataset select at runtime	frag_2.fastq
Step 3: Input dataset Input Dataset select at runtime	shortjump_1.fastq
Step 4: Input dataset Input Dataset select at runtime	shortjump_2.fastq
Step 5: Input dataset Input Dataset select at runtime	genome.fasta
Step 6: KmerFreq AR What type of data are you using? FASTQ library libraries 1 Forward FASTQ file Output dataset 'output' from step 1 Reverse FASTQ file Output dataset 'output' from step 2 Kmerfreq AR analysis to perform Consecutive Kmer size 17 Minimum precision kmer rate -1 ASCII shift of the quality value 33 Output kmers depth file? YES Total bases number used to get kmers None
Step 7: Corrector AR Corrector AR analysis to perform Consecutive List of input files Output dataset 'filelist' from step 6 Compressed frequency file of consecutive Kmer frequency data Output dataset 'cz' from step 6 Block length of consecutive kmer compressed file Output dataset 'cz_len' from step 6 Kmer size 17 Consecutive kmer low frequency cutoff 3 ASCII shift of the quality value 33 Correction AR settings to use Full parameter list Minimum length of a continuous high frequency Kmer region 10 Maximum number of bases that can be changed in a single read 2 Maximum number of bases allowed in a branch and bound tree 15000000 Remove low quality or suspicious data No Trim suspicious region at the end of reads according to Q_value? Yes - trim Q_value to less than or equal 2 continues region Trim error bases with Q value until it is less than or equal to 2 instead of correcting it No, correct this base Set quality threshold of error bases 30 Number of bases to trim from low quality read ends. Defaults to Kmer size/2 8 Minimum length of trimmed reads 50 Convert read1 and read2 corrected files into paired-end files Yes Output file format FASTQ compressed file
Step 8: SOAPdenovo2 Select a configuration file from history or create a new one? Create new configuration file Maximum read length 100 library libraries 1 Average insert size 180 Reverse sequence? forward-reverse Which operations should the reads be used for? For contig and scaffold assembly Length of base pairs to use from reads None Which order are the reads used while scaffolding 1 Pair number cutoff for a reliable connection None Length of contig that has to be aligned for a reliable read location None files files 1 What type of data are you using? Paired What is the format of your sequence data? FASTQ_GZIPPED Forward FASTQ Gzipped file Output dataset 'corrected_forward' from step 7 Reverse FASTQ Gzipped file Output dataset 'corrected_reverse' from step 7 libraries 2 Average insert size 3500 Reverse sequence? reverse-forward Which operations should the reads be used for? For only scaffold assembly Length of base pairs to use from reads None Which order are the reads used while scaffolding 2 Pair number cutoff for a reliable connection 11 Length of contig that has to be aligned for a reliable read location 31 files files 1 What type of data are you using? Paired What is the format of your sequence data? FASTQ Forward FASTQ file Output dataset 'output' from step 3 Reverse FASTQ file Output dataset 'output' from step 4 k-value in kmer 31 Delete kmers with frequency no larger than? 1 Resolve repeats by reads Yes Fill gaps in scaffold? Yes SOAP settings to use Default
Step 9: GapCloser 1.12 Scaffold file for gap closing Output dataset 'scafseq' from step 8 Select a configuration file from history or create a new one? Use one from history Select configuration file from history Output dataset 'config' from step 8 GapCloser settings to use Full parameter list Overlap parameter 31 Maximal read length 70
Step 10: Extract ACGT scaffolds Output dataset 'scaff' from step 9
Step 11: GAGE analysis Reference genome file in FASTA format Output dataset 'output' from step 5 Contig file in FASTA format Output dataset 'scafseq_gc_ctg_fa' from step 10 Scaffold file in FASTA format Output dataset 'scaff' from step 9
Step 12: stat GAGE output Output dataset 'outfile' from step 11

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peterli

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