Galaxy |

SSPACE (version 1.0.7)

Contigs FASTA file (-s):

Paired-end reads 1:

FASTA or FASTQ format

Paired-end reads 2:

FASTA or FASTQ format

Insert size:

Variability (e.g. 0.25 for 25%):

Orientation:

Extend the contigs using the paired reads (-x):

Uncheck for scaffolding only

Extension: minimum number of overlapping bases with the seed/contig during overhang consensus build up (-m):

E.g. 32-35 for 36bp reads

Extension: minimum number of reads needed to call an extension (-o):

Higher numbers increase reliability of the extension

Extension: maximum number of bases to trim on the contig end when all possibilities have been exhausted for an extension (-t):

Extension: unpaired reads (-u, optional):

FASTA or FASTQ format

Extension: minimum base ratio used to accept a overhang consensus base (-r):

Scaffolding: minimum number of links (read pairs) to compute scaffold (-k):

Scaffolding: maximum link ratio between two best contig pairs (-a):

Higher values lead to less accurate scaffolding

Scaffolding: minimum overlap required between contigs to merge adjacent contigs in a scaffold (-n):

Scaffolding: minimum contig length used for scaffold (-z):

Filters out contigs below this length. Leave empty or set to 0 for no filtering