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/ |
