Applied Genomics
Capacity Building
Genotyping Services
Public Domain
CFA - Molecular Breeding
Genome Sequences
Workshops / Conferences
5th NGGIBCI - 2015
4th NGGIBCI - 2014
VI ICLGG - 2012
3rd NGS Workshop - 2012
2nd NGS Workshop - 2010
1st NGS Workshop- 2009
2nd MAS Workshop- 2010
AAGB - 2008
Script Description
1 assemblathon_stats.pl - Extracts the assembly stats of a genome fasta file
2 batch_genscan.pl- Run the genscan gene prediction program in batch mode. Runs genscan as well as converts output to gff format.
3 extract_region.pl- Given a fasta and a coordinates file extracts the region corresponding to the coordinates
4 fastq2fasta.pl- Converts a fastq to fasta file
5 filterByLength.py- Filters a multifasta format file based on a length cutoff
6 genomeLength.py- Provides the lengths of chromosome as well as the total genome size
7 getReadLengths.py- Provides the lengths of the reads in a fastq file
8 gff2gtf.py- Converts gff format to the gtf file
9 NCBI_retrieval.pl- Retrieves the sequences (EST seq., unigenes, gene seq, books etc) from NCBI repository
10 seqtk- Post processign and format conversions of fasta/Fastq files
11 splitfasta.py- Split a multi fasta format file into individual fasta sequence files
12 vcfutils.pl- Format conversions and filtering of the vcf files
13 renamefq.py- Rename headers of a fastq file
14 extract_flanking_regions.pl- Extracts the regions of a fasta file with flanking regions from an assembly fasta file
15 ISMU_v1.0.tar.gz- ISMU pipeline – http://hpc.icrisat.cgiar.org/ISMU/
Please contact : Dr Rajeev Varshney, Director-Center of Excellence in Genomics, ICRISAT, Patancheru, 502 324, India;
Office: +91 40 3071 3305; Email : r.k.varshney@cgiar.org
© Center of Excellence in Genomics. 2008