GenomeAssemblyTools

This repository contains usefull python tools to deal with de novo genome assemblies using MUMmer4 and blast+.

Tools.py

• Contains the main functions and classes used by the other script.

Processing fasta files

extractFragment.py

• Extract a fragment of a fasta file (either a whole sequence, or a fragment of a sequence (1-based positions))

maskTelomeres.py

• Mask X kb at the start and end of each sequence of a fasta file.

reorderContigs.py

• Reorder contigs based on a reference genome. Usefull to have a clean diagonal when plotting against the reference.

renameContigs.py

• Rename contigs based on a reference genome.

Genome assembly filtering

filterContigSize.py

• Filter out contigs smaller than a specified threshold.

getNuclearContigs.py

• Retrieve contigs corresponding the nuclear genome, based on sequence similarity with a reference genome or a BLAST database containing nuclear chromosomes (several strain avoid reference bias).

removeRedundantContigs.py

• Remove contigs that are entirely covered by other contigs of the same assembly.

Genome assembly information

NbContigsToXCoverage.py

• Give the number of contig required to cover X% of a reference genome.

checkChromosomePresence.py

• Take a reference genome and indicate how many reference chromosomes are covered at X % (80% default) by the draft assembly. A detailled output (-i) gives the coverage of each chromosome of the reference.

findDoubleCentromeres.py

• Take the centromere sequence and indicate how many contigs contain more than 1 centromere.

findMergedChromosomes.py

• Give the number of contigs covering several reference chromosomes. Can be inacurate because of large translocation. Better use findDoubleCentromere.py to identify merged chromosomes.