Anuj Sharma rknx

A little bit of Javascript, little bit of android and a lot of Photoshop. Plant pathologist by training.

rknx / assem_mets.sh

Last active July 5, 2023 20:11

Fasta assembly metrics by assem_mets

	##/usr/bin/env bash

	# ------------------------------------------------------------------------------
	# Script: Assembly metrics
	# Author: Anuj Sharma
	# Github: rknx/
	# Email: [email protected]
	# Description: This script is used to calculate various assembly metrics from
	# a single multiFASTA file, often a genome assembly.
	# Last modified: <2022/08/04>

rknx / FastaToSNPCount.sh

Created October 13, 2022 05:19

Pairwise mismatch count from multifasta alignment

	#!/bin/bash

	#########################################
	# Anuj Sharma #
	# [email protected] #
	# 2022-10-13 #
	#########################################

	# Usage: FastaToSNPCount.sh <input.fasta>

rknx / roary2ffn.sh

Last active June 24, 2022 22:25

Extracting nucleotide sequence from ffn files following Roary

	#!/bin/bash

	#########################################
	# Anuj Sharma #
	# [email protected] #
	# 2022-05-18 #
	#########################################

	# Reading the input parameters
	OPTIND=1

rknx / alien_intersect.sh

Last active October 14, 2022 05:34

Intersect genes (gtf/gff) with alien_hunter output

	#!/bin/bash

	#########################################
	# Anuj Sharma #
	# [email protected] #
	# 2022-06-24 #
	#########################################

	# Reading the input parameters

rknx / gff2gtf.sh

Created January 4, 2022 20:53

Convert GFF3 file to GTF2.5

	#!/bin/bash

	########## Anuj Sharma ##########
	########## [email protected] ##########
	########## github/rknx ##########
	########## 2022/01/04 ##########

	[[ -z "$1" ]] && echo "Usage: gff2gtf.sh in.gff > out.gtf" >&2 && exit
	[[ ! -s "$1" ]] && echo "Provide valid input file" >&2 && exit