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MaSuRCA (version 4.0.6+galaxy0)

Paired-end reads:

Select between paired and paired collection

Select unpaired reads:

Specify dataset with unpaired reads

Mean size:

Libarary insert average length

Standard deviation:

Library insert standard deviation - if not known, set it to approximately 15% of the mean

Use Nanopore long reads:

Optional Nanopore reads must be in a single fasta or fastq file

Use Pacbio long reads:

Optional Pacbio reads must be in a single fasta or fastq file

Synteny-assisted assembly:

Concatenate all reference genomes into one reference.fa; works for Illumina-only data

Jellyfish hash size:

Set this to about 10x the genome size

MEGA_READS_ONE_PASS:

set to 0 (default) to do two passes of mega-reads for slower, but higher quality assembly, otherwise set to 1

Set this to use Flye assembler for final assembly of corrected mega-reads:

If you are doing Hybrid Illumina paired end + Nanopore/PacBio assembly ONLY (no Illumina mate pairs or OTHER frg files). DO NOT use if you have less than 15x coverage by long read

Include Linking Mates:

Most of the paired end reads end up in the same super read and thus are not passed to the assembler. Those that do not end up in the same super read are called ”linking mates” . The best assembly results are achieved by setting this parameter to 1 for Illumina-only assemblies. If you have more than 2x coverage by long reads, set this to 0.

MaSuRCA

This implementation of MaSuRCA uses a config file for more complicated assemblies and to change default settings. Illumina reads (mandatory) and long reads from PACBIO or Oxford Nanopore or both can be included. It is written by Aleksey Zimin at Johns Hopkins University. Included below is relevant notes from MaSuRCA's github page.

Input data

The following types of data are supported:

Illumina paired end (or single end) reads -- MANDATORY. The mean and stdev parameters are the library insert average length and standard deviation. If the standard deviation is not known, set it to approximately 15% of the mean.If the second (reverse) read set is not available, do not specify it and just specify the forward reads. Files must be in fastq format and can be gzipped.

PacBio/MinION data are supported. Note that you have to have 50x + coverage in Illumina Paired End reads to use PacBio of Oxford Nanopore MinION data. Supply PacBio or MinION reads in a single fasta or fastq file (can be gzipped).

Parameters

The following parameter is mandatory:

jellyfish hash size, set this to about 10x the genome size.

Optional parameters:

linking mates: Most of the paired end reads end up in the same super read and thus are not passed to the assembler. Those that do not end up in the same super read are called ”linking mates” . The best assembly results are achieved by setting this parameter to 1 for Illumina-only assemblies. If you have more than 2x coverage by long (454, Sanger, etc) reads, set this to 0.