Galaxy | Tool Preview

metaplasmidSPAdes (version 3.15.5+galaxy2)
To run read error correction, reads should be in FASTQ format.
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.
In paired-end sequencing, the library preparation yields a set of fragments, and the machine sequences each fragment from both ends. In mate-pair sequencing, the library preparation yields two fragments that are distal to each other in the genome and in the opposite in orientation to that of a mate-paired fragment.
Note: mate-pair fragments are generally in a RF conformation. In general, paired-end reads tend to be in a FR orientation.
If the reads have been generated from the same sample, it means that they belong to the same library.
Enable this option if you want to combine to data sources (e.g. single and paired reads).
Additional read files
Additional read files 0
Comma-separated list, all values must be odd, less than 128 and listed in ascending order.
Phred quality offset in the input reads. Default: auto-detect
Error correction requires FASTQ input files.
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.

metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data sets.


SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.

To run SPAdes 3.15.3 you need at least one library of the following types:

SPAdes supports mate-pair only assembly. However, we recommend to use only high-quality mate-pair libraries in this case (e.g. that do not have a paired-end part). We tested mate-pair only pipeline using Illumina Nextera mate-pairs.


A detailed description can be found in the input section of the manual.



More information can be found on github.