中文说明

split large genome fasta and gtf/gff into shorter scaffolds

• Large genome (e.g. wheat) have long single chromosome, which some software or file format not support.
• .bai (bam index file) only support chromosomes shorter than $2^{29}-1$ bp.
• .csi extend the limit to $2^{44}-1$ bp, but support for .csi is not widely applied in all softwares.
• .tbi (variant index file) have the same limitation, but the extended .csi format is not supported by some software (like GATK).

Summary

This script can :

1. split the genome sequences (fasta format) into smaller scaffolds
2. split point is always the GAP sequence (a certain length of Ns)
3. the gtf/gff chromosome name and feature coordinates can be converted simultaneously.(optional)

Usage

Installation

1. download repository as zip
2. unzip splitLargeGenome-main.zip
3. just run.

perl splitLargeGenome-main/splitLargeGenome.pl

Options

    -fa        <file>      required       input genome sequences file, fasta format
    -gxf       <file>      optional       gtf/gff file for the fasta file, default not set
    -out       <str>       required       output file prefix
    -numN      <num>       optional       minimum length of Ns as Separator, default 10
    -minlen    <num>       optional       minmum  scaffold length in output, default 300000000
    -maxlen    <num>       optional       maximum fragment length in output, default 500000000

Use example

Split a genome into smaller fragments of 300M~500M in length using at least 10 Ns as separators, and update the corresponding gene.gtf with the new coordinates

perl  splitLargeGenome.pl  -fa genome.fa -minlen 300000000 -maxlen 500000000 -gxf gene.gtf -out genome.sep  -numN 10

Results

genome.sep.fa         : scaffold sequences with length between 300~500Mb
genome.sep.detail.txt : split position details
gene.sep.gtf          : new gtf file with new positions according to the detail file
                         only exists when -gxf was set

report bugs

any suggestions or bug reports you can:

• raise an issue
• send an email