Documentation
Algorithm Based Automatic Contiguation of Assembled Sequences
Given an assembly in FASTA format, output a descaffolded assembly.
Given a fastq file, it performs digital normalisation on the reads using khmer
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 a fastq file(s), perform SGA preprocessing and error correction
Given a forward and reverse FASTQ file and a file with primers, it will remove the primers if it appears within a specified distance from the beginning of the read
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.
Remove adapter sequences from paired reads using Trimmomatic
Performs SGA error correction on the reads
Run SGA preprocess and error correction steps
Preprocess reads before error correction
Wrapper around circlator
Perform digital normalisation on sequencing reads
Create the config file thats used to drive GapFiller
Iteratively close gaps
Run a single iteration of gapfiller
Wrapper around iva_qc
Update the names of the contigs so that the assembly can be submitted to a database like EMBL
Remove a set of specified primers from the edges of a read using QUASR
Wrapper around the quiver call
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
Utilities for sequences in a FASTA file
Take a fastq file and calculate some useful statistics and values
Role for getting the read lengths from a fastq file (useful when reads are of varying lengths)
Sorts a fasta file by sequence length
Role for unzipping files if needed
Validates the executable is available in the path before running it.