# HG changeset patch # User slegras # Date 1443383569 14400 # Node ID 1405432d1b9c0d2243ebe4ecfb2dabbc467411e6 Uploaded diff -r 000000000000 -r 1405432d1b9c sickle.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sickle.xml Sun Sep 27 15:52:49 2015 -0400 @@ -0,0 +1,254 @@ + + Windowed Adaptive Trimming of FastQ data + + sickle + + + sickle + + #if str($readtype.single_or_paired) == "se": + se -f $input_single -o $output_single + + #if $input_single.ext == "fastq": + -t sanger + #else if $input_single.ext == "fastqsanger": + -t sanger + #else if $input_single.ext == "fastqillumina": + -t illumina + #else if $input_single.ext == "fastqsolexa": + -t solexa + #end if + + #end if + + #if str($readtype.single_or_paired) == "pe_combo": + #if $readtype.output_n: + pe -c $input_combo -M $output_combo + #else + pe -c $input_combo -m $output_combo -s $output_combo_single + #end if + + #if $input_combo.ext == "fastq": + -t sanger + #else if $input_combo.ext == "fastqsanger": + -t sanger + #else if $input_combo.ext == "fastqillumina": + -t illumina + #else if $input_combo.ext == "fastqsolexa": + -t solexa + #end if + + #end if + + #if str($readtype.single_or_paired) == "pe_sep": + pe -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single + + #if $input_paired1.ext == "fastq": + -t sanger + #else if $input_paired1.ext == "fastqsanger": + -t sanger + #else if $input_paired1.ext == "fastqillumina": + -t illumina + #else if $input_paired1.ext == "fastqsolexa": + -t solexa + #end if + + #end if + + #if str($qual_threshold) != "": + -q $qual_threshold + #end if + + #if str($length_threshold) != "": + -l $length_threshold + #end if + + #if $no_five_prime: + -x + #end if + + #if $trunc_n: + -n + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (readtype['single_or_paired'] == 'se') + + + + (readtype['single_or_paired'] == 'pe_combo') + + + + (readtype['single_or_paired'] == 'pe_combo') + (readtype['output_n'] == False) + + + + (readtype['single_or_paired'] == 'pe_sep') + + + + (readtype['single_or_paired'] == 'pe_sep') + + + + (readtype['single_or_paired'] == 'pe_sep') + + + + +**Sickle - A windowed adaptive trimming tool for FASTQ files using quality** + +.. class:: infomark + +**About** + +Most modern sequencing technologies produce reads that have +deteriorating quality towards the 3'-end and some towards the 5'-end +as well. Incorrectly called bases in both regions negatively impact +assembles, mapping, and downstream bioinformatics analyses. + +Sickle is a tool that uses sliding windows along with quality and +length thresholds to determine when quality is sufficiently low to +trim the 3'-end of reads and also determines when the quality is +sufficiently high enough to trim the 5'-end of reads. It will also +discard reads based upon the length threshold. It takes the quality +values and slides a window across them whose length is 0.1 times the +length of the read. If this length is less than 1, then the window is +set to be equal to the length of the read. Otherwise, the window +slides along the quality values until the average quality in the +window rises above the threshold, at which point the algorithm +determines where within the window the rise occurs and cuts the read +and quality there for the 5'-end cut. Then when the average quality +in the window drops below the threshold, the algorithm determines +where in the window the drop occurs and cuts both the read and quality +strings there for the 3'-end cut. However, if the length of the +remaining sequence is less than the minimum length threshold, then the +read is discarded entirely (or replaced with an "N" record). 5'-end +trimming can be disabled. Sickle also has an option to truncate reads +with Ns at the first N position. + +Sickle supports three types of quality values: Illumina, Solexa, and +Sanger. Note that the Solexa quality setting is an approximation (the +actual conversion is a non-linear transformation). The end +approximation is close. Illumina quality refers to qualities encoded +with the CASAVA pipeline between versions 1.3 and 1.7. Illumina +quality using CASAVA >= 1.8 is Sanger encoded. The quality value will +be determined from the datatype of the data, i.e. a fastqsanger datatype +is assumed to be Sanger encoded. + +Note that Sickle will remove the 2nd fastq record header (on the "+" +line) and replace it with simply a "+". This is the default format for +CASAVA >= 1.8. + +----- + +.. class:: infomark + +**Options** + +**Single-end** + +This option takes one single-end input file and outputs one single-end +output file of reads that passed the filters. + +**Paired-End (one interleaved input file)** + +This option takes as input one interleaved paired-end file. If you then +check the "Output only one file with all reads" checkbox, it will output +one interleaved file where any read that did not pass filter will be replaced +with a FastQ record where the sequence is a single "N" and the quality is the +lowest quality possible for that quality type. This will preserve the paired +nature of the data. If you leave the checkbox unchecked, it will output two files, +one interleaved file with all the passed pairs and one singletons file where only +one of the pair passed filter. + +**Paired-End (two separate input files)** + +This option takes two separate (forward and reverse) paired-end files as input. +The output is three files: Two paired-end files with pairs that passed filter and +a singletons file where only one of the pair passed filter. + +**Quality threshold** + +Input your desired quality threshold. This threshold is phred-scaled, which is typically +values between 0-41 for FastQ data. + +**Length threshold** + +Input your desired length threshold. This is the threshold to determine if a read is kept +after all the trimming steps are done. + +**Disable 5-prime trimming** + +An option to disable trimming the read on the 5-prime end. This trimming trims the read +if the average quality values dip below the quality threshold at the 5-prime end. + +**Truncate sequences with Ns** + +This option will trim a read at the first "N" base in the read after doing quality trimming. +It is then still subject to the length threshold. + +----- + +.. class:: infomark + +**Citation** + +Sickle doesn't have a paper, but you can cite it like this:: + + Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files + (Version 1.33) [Software]. Available at https://github.com/najoshi/sickle. + +----- + +Copyright: Nikhil Joshi + +http://bioinformatics.ucdavis.edu + +http://github.com/ucdavis-bioinformatics + +http://github.com/najoshi + + + + diff -r 000000000000 -r 1405432d1b9c tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Sep 27 15:52:49 2015 -0400 @@ -0,0 +1,6 @@ + + + + + +