Documentation
Algorithm Based Automatic Contiguation of Assembled Sequences
Given an assembly in FASTA format, output a descaffolded assembly.
Given an assembly iteratively fill gaps
Given an assembly, some reads and optionally a reference, reduce the number of contigs and fill gaps.
Given an assembly and a reference, order the contigs
Given two fastq files (forward and reverse), try and correct the reads using SGA before doing the assembly
Given an assembly, rename the contigs iteratively
Given an assembly and some reads in fastq format, try and scaffold the assembly.
Modules
Improve an assembly by scaffolding, contig ordering and gap closing.
Moose Role for putting in delimiters for Abacas to join up contigs
Iteratively run abacas to order contigs
Wrapper script for Abacas, just runs it in a separate directory.
Performs SGA error correction on the reads
Run SGA preprocess and error correction steps
Preprocess reads before error correction
Create the config file thats used to drive GapFiller
Iteratively close gaps
Run a single iteration of gapfiller
Update the names of the contigs so that the assembly can be submitted to a database like EMBL
Given a fasta file as input, output a descaffolded multi-fasta file.
Create the config file thats used to drive SSpace
Iteratively run SSpace.
Run one iteration of SSpace
Role for handling output filenames
Make sure the input files are in the correct format, and paths are resolved.
Role for handling temp directories
Role for unzipping files if needed
Validates the executable is available in the path before running it.