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Get a GFA file from a FASTA file containing 'Ns' regions

fasta2bed.py

The fasta2bed.py script takes as input a FASTA file and converts it to a BED file containing the 'N's coordinates for each scaffold. It can be run with the following command:

fasta2bed.py -fa referenceGenome.fasta -out targetSequenceCoordinates.bed
  • referenceGenome.fasta: FASTA file containing the sequences of the scaffolds (reference genome)
  • targetSequenceCoordinates.bed: Output BED file

The format of the output BED file is: <scaffoldID> <Nstretch_startPosition> <Nstretch_endPosition>

bed2gfa.py

The bed2gfa.py script converts a BED file containing the 'N's coordinates for each scaffold (or locus coordinates) to a GFA file (GFA 2.0).
It is possible to filter the 'N's regions you want to treat as gaps by:

  • their size (e.g. gap lengths)
  • the flanking contigs' sizes (for example, select only the 'N's regions whose flanking contigs' sizes are long enough to get enough barcodes)

It can be run with the following command:

bed2gfa.py -bed targetSequenceCoordinates.bed -fa referenceGenome.fasta -out targetSequenceCoordinates.gfa -min MIN_GAPLENGTH -max MAX_GAPLENGTH -contigs MIN_CONTIGSIZE
  • targetSequenceCoordinates.bed: BED file containing the 'Ns' coordinates for each scaffold
  • referenceGenome.fasta: FASTA file containing the sequences of the scaffolds (reference genome)
  • targetSequenceCoordinates.gfa: Output GFA file
  • MIN_GAPLENGTH: Minimum size of the 'N's region to treat as a gap
  • MAX_GAPLENGTH: Maximum size of the 'N's region to treat as a gap
  • MIN_CONTIGSIZE: Minimum size of the flanking contigs of the 'N's region to treat as a gap

The output GFA file is a GFA 2.0 file.

Get a GFA file from a file containing the paths between scaffolds

paths2gfa.py

The paths2gfa.py script takes as input a file containing the paths between scaffolds and converts it to a GFA file (GFA 2.0). It can be run with the following command:

paths2gfa.py -fa referenceGenome.fasta -paths pathsFile.txt -out targetSequenceCoordinates.gfa
  • referenceGenome.fasta: FASTA file containing the sequences of the scaffolds (reference genome)
  • pathsFile.txt: File containing the paths between scaffolds
  • targetSequenceCoordinates.gfa: Output GFA file

The format of the input PATHS file is: <numberOfScaffolds>****<sid1(f|r)>+<sid2(f|r)>
When the orientation of the scaffold is undetermined (?), both forward and reverse orientations are taken into consideration.
The output GFA file is a GFA 2.0 file.

Get a GFA file from a matrix file containing the links between the ends of the scaffolds

matrix2gfa.py

The matrix2gfa.py script takes as input a file containing the number of common barcodes between all possibles pairs of scaffolds' extremities (links between the ends of the scaffolds) in tabular format (matrix) and converts it to a GFA file (GFA 2.0). It can be run with the following command:

matrix2gfa.py -fa referenceGenome.fasta -matrix matrixFile.matrix -out targetSequenceCoordinates.gfa -threshold THRESHOLD
  • referenceGenome.fasta: FASTA file containing the sequences of the scaffolds (reference genome)
  • matrixFile.matrix: File containing the number of common barcodes between all possibles pairs of scaffolds' extremities (matrix)
  • targetSequenceCoordinates.gfa: Output GFA file
  • THRESHOLD: Minimal number of links two scaffolds must share to try to fill the gap between them

The format of the input MATRIX file is: <scaffoldLeftID>:<extremitiesCoordStart>-<extremitiesCoordEnd> <scaffoldRightID>:<extremitiesCoordStart>-<extremitiesCoordEnd> <numberOfCommonBarcodes>
The output GFA file is a GFA 2.0 file.

Get a GFA file from a VCF file containing Indels coordinates

vcf2gfa.py

The vcf2gfa.py script converts a VCF file containing the Indels coordinates to a GFA file (GFA 2.0).
It is possible to filter the Indels you want to treat as targets (e.g. you want to reconstruct) by:

  • the flanking contigs' sizes (for example, select only the Indels whose flanking contigs' sizes are long enough to get enough barcodes)

It can be run with the following command:

vcf2gfa.py -vcf vcfFile.vcf -fa referenceGenome.fasta -out indelSequenceCoordinates.gfa -contigs MIN_CONTIGSIZE
  • vcfFile.vcf: VCF file containing the Indels coordinates
  • referenceGenome.fasta: FASTA file of the reference genome
  • indelSequenceCoordinates.gfa: Output GFA file
  • MIN_CONTIGSIZE: Minimum size of the flanking contigs of the Indels to treat as a target

The output GFA file is a GFA 2.0 file.

Merge two GFA 2.0 files together

mergegfa.py

The mergegfa.py script takes as input two GFA files (GFA 2.0) and merge them together. It can be run with the following command:

mergegfa.py -1 gfaFile1.gfa -2 gfaFile2.gfa -out merged_gfa.gfa
  • gfaFile1.gfa: GFA 2.0 file n°1
  • gfaFile2.gfa: GFA 2.0 file n°2
  • merged_gfa.gfa: Output merged GFA file

The output GFA file is a GFA 2.0 file.

Convert a GFA 2.0 file to a FASTA file

gfa2tofasta.py

The gfa2tofasta.py script takes as input a GFA file (GFA 2.0) and converts it to a FASTA file. The gaps of the GFA file are returned as 'N's regions in the output FASTA file. It can be run with the following command:

gfa2tofasta.py -in gfaFile.gfa -out fastaFile.fasta
  • gfaFile.gfa: GFA 2.0 file
  • fastaFile.fasta: Output FASTA file