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FLASH
PERF
pipeline
Input sequences in the FASTQ format
Past paired-end reads in FASTQ format (
example
)in both boxes respectively. Click(
clear
) to clear the content.
*
User only needs to choose one of two operations (input sequences and upload files)
Or upload files
*
Please choose two FASTQ format files storing the forward and reverse reads respectively(the size of each file <30M).
Common parameters
-m: The minimum required overlap length between two reads to provide a confident overlap
-M: Maximum overlap length expected in approximately 90% of read pairs
-x: Maximum allowed ratio between the number of mismatched base pairs and the overlap length
-p: The smallest ASCII value of the characters used to represent quality values of bases in FASTQ files
Other parameters
-O: FLASH uses the same parameters when trying each orientation
No
Yes
-r: Read length
-f: Fragment length
-s: Fragment standard deviation
--cap-mismatch-quals: Calculate such scores as max(|q1 - q2|, 2)
No
Yes
-z: Compress the output files directly with zlib, using the gzip container format
No
Yes
Submit the job
You can provide your email and we will notify you after work.(Recomended)
Submit
Reset
Input sequences in the FASTA format
Paste DNA sequences in FASTA format (
example
). Click(
clear
) to clear the content.
*
Or upload files
*
User only needs to choose one of two operations (input sequences or upload files (the size of each file <30M))
Common parameters
-l: Minimum length cutoff of repeat
-u: Minimum number of repeating units to be considered
-rep: File with list of repeats (Not allowed with -m and/or -M)
-m: Minimum size of a repeat motif in bp (Not allowed with -rep)
-M: Maximum size of a repeat motif in bp (Not allowed with -rep)
-s: Minimum size of sequence length for consideration (in bp)
-S: Maximum size of sequence length for consideration (in bp)
-f: Filter some sequences that we don't need to analyze by id
-F: Specify some sequences we need to analyze by id
-a: Generate a summary HTML report
No
Yes
Submit the job
You can provide your email and we will notify you after work.(Recomended)
Submit
Reset
Input sequences in the FASTQ format
Paste DNA sequences in FASTQ format (
example
). Click(
clear
) to clear the content.
*
Or upload files
*
User only needs to choose one of two operations (input sequences and upload files)
Please choose both FASTQ format files storing the forward and reverse reads respectively (the size of each file <30M).
Common parameters
-fl: Length of terminal flanking sequences
-fm: The minimum required overlap length between two reads to provide a confident overlap
-fM: Maximum overlap length expected in approximately 90% of read pairs
-x: Maximum allowed ratio between ">-fx: Maximum allowed ratio between the number of mismatched base pairs and the overlap length.
-fp: The smallest ASCII value of the characters used to represent quality values of bases in FASTQ files
-pl: Minimum length cutoff of repeat
-pu: Minimum number of repeating units to be considered
-prep: File with list of repeats (Not allowed with -m and/or -M)
-pm: Minimum size of a repeat motif in bp (Not allowed with -rep)
-pM: Maximum size of a repeat motif in bp (Not allowed with -rep)
-ps: Minimum size of sequence length for consideration (in bp)
-pS: Maximum size of sequence length for consideration (in bp)
-pf: Filter some sequences that we don't need to analyze by id
-pF: Specify some sequences we need to analyze by id
-pa: Generate a summary HTML report
No
Yes
Other parameters
-fr: Read length
-ff: Fragment length
-fs: Fragment standard deviation
--fcap-mismatch-quals: Calculate such scores as max(|q1 - q2|, 2)
No
Yes
Submit the job
You can provide your email and we will notify you after work.
Submit
Reset
