README.md

Riddikulus

Helpful bioinformatics scripts

blastn_to_fasta.sh

Script to perform blastn, using only one gene as input and several genomes and then parse blast alignments into multifasta

Usage example:

./blastn_to_fasta.sh -gene gene.fasta -genomes_file genome_list.txt -threads 1 -min_qc 60 -min_ident 70

Options:

./blastn_to_fasta.sh
 -gene gene.fasta                - query fasta file with single sequence
 -genomes_file genome_list.txt   - list of path to genomes' files in fasta format. One path per line.  
 -threads 1                      - integer number of threads to use
 -min_qc 60                      - minimum query coverage per high-scoring segment pair (float value)
 -min_ident 70                   - minimum percent of identity of BLAST hits (float value)

Output:

*_tab - tab-formatted BLASTn output
*.bed - bed-files with alignment' coordinates
*.fasta - fasta with sequences, extracted according to coordinates 
*_blastn.fasta - resulting multifasta with all hits in all genomes

Tested with:

BLAST 2.9.0
bedtools v2.27.1
samtools v1.7

pilon_polish.sh

Performs polishing with Pilon

Usage example:

bash ../polish.sh -reference my_genome.fasta -1 forward_reads.fq -2 reverse_reads.fq -num_iterations 10 -prefix_name test_pilon

Parameters:

-reference - draft genome to polish (.fasta, .fna, etc.)
-1, -2 - forward and reverse reads, respectively ( fastq, fq, fq.gz  ..)
-num_iterations - number of polishing iterations <int>
-prefix_name - prefix for temporary (.bam) files

Output:

.fasta - polished contigs
.bed - aligned reads to contigs