This is a collection of helpful assembly scripts and utilities for use in assembling the genomes of plant forage species.
This repository currently consists of two Perl scripts that provide general utility for the assembly of Eukaryotic species genomes. Both scripts supply usage statements and require only a base installation of Perl v5.8+. Here is a brief summary of the usage statements:
perl ./perl_scripts/alignAndOrderSnpProbes.pl
Input:
-a <Assembly fasta file> AND -p <Probe fasta file>
OR
-n <Nucmer alignment format>
OR
-g <Blast alignment format> AND -m <alignment length to filter (int)>
Optional:
-c <circos flag>
AND
-f <query fasta samtools fai file>
AND
-r <reference fasta samtools fai file>
Output:
-o <Base name for all output files>perl ./perl_scripts/filterOverhangAlignments.pl <input overhang PAF file> <the original full PAF file> <output file name>Note: depends on the following scripts/programs being installed on your PATH and set to executable status:
- https://github.com/njdbickhart/perl_toolchain/blob/master/bed_cnv_fig_table_pipeline/nameListVennCount.pl
- https://github.com/njdbickhart/python_toolchain/blob/master/utils/tabFileColumnCounter.py
- generate_pairs.pl (this repository)
- https://github.com/lh3/minimap2
bash bac_end_characterization.sh <input forward BAC end fasta> <input reverse BAC end fasta> <Reference assembly fasta> <output prefix>Output is a brief table named (output_prefix).final.tab that contains category counts for BAC end mappings.