/shell_scripts

Collection of shell scripts used to run analyses on SLURM system.

Primary LanguageShell

shell_scripts

A collection of shell scripts used to run analyses on a SLURM-based HPC cluster.

Read QC

Count Nucelotides
FastQC
Filtlong
Nanoplot
Porechop
Singe to Multi fast5
Trimmomatic

Genome Assembly

Long Polish (Racon x1 & Medaka x1)
NECAT
Pilon
Purge Dups
RaGOO
RagTag
Raven
SPAdes
Trycycler

Genome Comparison

ANI
Circos
Dotplot

Genome QC

Assembly Stats
BUSCO
CheckM
HapDup
Happy
KAT

Genome Annotation

BRAKER
Prokka
Red
Longest Isoform

RNA-seq

bamCoverage
featureCounts
HISAT2
HTSeq-Count
Salmon
StringTie

Ortholog Analysis

BUSCO
OrthoFinder

Phylogenies

BUSCO Phylogenetics
Orthofinder
SANS Genome
SNP RAxML

Variant Analysis

LRA
Medaka
SVIM