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rnaSPAdes (version 3.15.5+galaxy2)

Single-end or paired-end short-reads:

It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.

FASTQ RNA-seq file(s):

Use an additional set of short-reads:

Enable this option if you want to combine to data sources (e.g. single and paired reads).

Additional read files

Additional read files 0

Select k-mer detection option:

By default rnaSPAdes uses 2 k-mer sizes, which are automatically detected using read length (approximately one third and half of the maximal read length). We recommend not to change this parameter because smaller k-mer sizes typically result in multiple chimeric (misassembled) transcripts. Comma-separated list, all values must be odd, less than 128 and listed in ascending order.

Set Phred quality offset:

Phred quality offset in the input reads. Default: auto-detect

Set strand specificity:

rnaSPAdes supports strand-specific RNA-Seq datasets. Use 'RF' when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and 'FR' otherwise. If the dataset is single-end use 'FR' option in case when reads correspond to gene strand and 'RF' otherwise. Note: strand-specificity is not related and should not be confused with FR and RF orientation of paired reads. RNA-Seq paired-end reads typically have forward-reverse orientation, which is assumed by default and no additional options are needed

Pipeline options:

Error correction requires FASTQ input files.

Select optional output file(s):

Only shown in history if selected here and generated by the specific run.

What it does

SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.

rnaSPAdes is a subtool for de novo transcriptome assembly from RNA-Seq data and is suitable for all kinds of organisms.

Input

rnaSPAdes take as an input at least one paired-end or single-end library. For hybrid assembly you can use PacBio or Oxford Nanopore reads.

In case you have sequenced several RNA-Seq libraries using the same protocol from different tissues / conditions, and the goal as to assemble a total transcriptome, we suggest to provide all files as a single library. Note, that sequencing using the same protocol implies that the resulting reads have the same length, insert size and strand-specificity. Transcript quantification for each sample can be done afterwards by separately mapping reads from each library to the assembled transcripts.

Output

Assembly graph
Assembly graph with scaffolds
Corrected reads by BayesHammer
Hard filtered transcripts includes only long and reliable transcripts with rather high expression
Log file
Soft filtered transcripts includes short and low-expressed transcipts, likely to contain junk sequences
Transcripts
Transcripts paths

References

More information can be found on on github.