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metaplasmidSPAdes (version 3.15.5+galaxy2)

Operation mode:

To run read error correction, reads should be in FASTQ format.

Pair-end reads input 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.

FASTQ file(s): forward reads:

FASTQ file(s): reverse reads:

Type of paired-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.

Select orientation of reads:

Note: mate-pair fragments are generally in a RF conformation. In general, paired-end reads tend to be in a FR orientation.

The samples belong to the same library:

If the reads have been generated from the same sample, it means that they belong to the same library.

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:

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

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.

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

Input

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:

Illumina paired-end/high-quality mate-pairs/unpaired reads
IonTorrent paired-end/high-quality mate-pairs/unpaired reads
PacBio CCS reads
Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.

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.

Notes:

It is strongly suggested to provide multiple paired-end and mate-pair libraries according to their insert size (from smallest to longest).
It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5).
We suggest not to run SPAdes on PacBio reads for large genomes.
SPAdes accepts gzip-compressed files.

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

Output

Contigs
Contigs stats
Corrected reads by BayesHammer
Log file
Scaffolds (recommended for use as resulting sequences)
Scaffolds stats

References

More information can be found on github.