Scripts

Script Description
assemblathon_stats.pl  Extracts the assembly stats of a genome fasta file
batch_genscan.pl Run the genscan gene prediction program in batch mode. Runs genscan as well as converts output to gff forma
extract_region.pl Given a fasta and a coordinates file extracts the region corresponding to the coordinates
fastq2fasta.pl Converts a fastq to fasta file
filterByLength.py Filters a multifasta format file based on a length cutoff
genomeLength.py Provides the lengths of chromosome as well as the total genome size
getReadLengths.py Provides the lengths of the reads in a fastq file
gff2gtf.py Converts gff format to the gtf file
NCBI_retrieval.pl Retrieves the sequences (EST seq., unigenes, gene seq, books etc) from NCBI repository
seqtk Post processing and format conversions of fasta/Fastq files
splitfasta.py Split a multi fasta format file into individual fasta sequence files
vcfutils.pl Format conversions and filtering of the vcf files
renamefq.py Rename headers of a fastq file
extract_flanking_regions.pl Extracts the regions of a fasta file with flanking regions from an assembly fasta file
ISMU_v1.0.tar.gz ISMU pipeline – http://hpc.icrisat.cgiar.org/ISMU/
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