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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: rknx@outlook.com
# 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
rknx / FastaToSNPCount.sh
Created October 13, 2022 05:19
Pairwise mismatch count from multifasta alignment
#!/bin/bash
#########################################
# Anuj Sharma #
# rknx@outlook.com #
# 2022-10-13 #
#########################################
# Usage: FastaToSNPCount.sh <input.fasta>
@rknx
rknx / roary2ffn.sh
Last active June 24, 2022 22:25
Extracting nucleotide sequence from ffn files following Roary
#!/bin/bash
#########################################
# Anuj Sharma #
# rknx@outlook.com #
# 2022-05-18 #
#########################################
# Reading the input parameters
OPTIND=1
@rknx
rknx / alien_intersect.sh
Last active October 14, 2022 05:34
Intersect genes (gtf/gff) with alien_hunter output
#!/bin/bash
#########################################
# Anuj Sharma #
# rknx@outlook.com #
# 2022-06-24 #
#########################################
# Reading the input parameters
@rknx
rknx / gff2gtf.sh
Created January 4, 2022 20:53
Convert GFF3 file to GTF2.5
#!/bin/bash
########## Anuj Sharma ##########
########## rknx@outlook.com ##########
########## 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