Galaxy | Accessible Workflow | Metagenomics Kraken Healthy workflow

Metagenomics Kraken Healthy workflow

Annotation: Hisat2, fastqtosam, sortsam, mark and remove duplicates, split in 2 fastq, Kraken

Step	Annotation
Step 1: Input dataset collection input select at runtime
Step 2: HISAT2 Source for the reference genome Use a built-in genome Select a reference genome hg38 Is this a single or paired library Paired-end Dataset Collection Paired Collection Output dataset 'output' from step 1 Specify strand information Unstranded Paired-end options Use default values Summary Options: Output alignment summary in a more machine-friendly style. True Print alignment summary to a file. False Advanced Options: Input options Use default values Alignment options Use default values Scoring options Use default values Spliced alignment options Use default values Reporting options Use default values Output options Specify output options Write unaligned reads (in fastq format) to separate file(s) True Write aligned reads (in fastq format) to separate file(s) False Other options Use default values Job Resource Parameters Use default job resource parameters
Step 3: FastqToSam What is your input data Paired end (two datasets) Input fastq file for the first read in paired end data Output dataset 'output_unaligned_reads_r' from step 2 Input fastq file for the second read of paired end data Output dataset 'output_unaligned_reads_l' from step 2 Select quality encoding scheme Sanger (+33) Read group name A Sample name sample-a The library name Empty. The platform unit (often run_barcode.lane) Empty. The platform type (e.g. illumina, 454) Empty. The sequencing center from which the data originated Empty. Predicted median insert size, to insert into the read group header Not available. Comment to include in the output dataset's header Empty. Optional description information Empty. Run date Empty. Minimum quality allowed in the input fastq 0 Minimum quality allowed in the input fastq 93 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name False Allow (and ignore) empty lines False Select validation stringency Lenient
Step 4: SortSam Select SAM/BAM dataset or dataset collection Output dataset 'outFile' from step 3 Sort order Coordinate Select validation stringency Lenient
Step 5: MarkDuplicates Select SAM/BAM dataset or dataset collection Output dataset 'outFile' from step 4 Comments If true do not write duplicates to the output file instead of writing them with appropriate flags set True Assume the input file is already sorted True The scoring strategy for choosing the non-duplicate among candidates SUM_OF_BASE_QUALITIES Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset Empty. The maximum offset between two duplicte clusters in order to consider them optical duplicates 100 Barcode Tag Empty. Select validation stringency Lenient
Step 6: bedtools Convert from BAM to FastQ Convert the following BAM file to FASTQ Output dataset 'outFile' from step 5 Create FASTQ based on the mate info in the BAM R2 and Q2 tags. False FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option. True
Step 7: Kraken Single or paired reads Paired Forward strand Output dataset 'output' from step 6 Reverse strand Output dataset 'output2' from step 6 Verify read names match False Output classified and unclassified reads? True Enable quick operation No Print no Kraken output for unclassified sequences False Select a Kraken database bacteria Job Resource Parameters Use default job resource parameters

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sguauque

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