Currently Available Pipelines

Currently Available Pipelines#

Pipeline

Description

annotate-braker3

Annotate an assembly using BRAKER3

annotate-braker3-isoseq

Annotate an assembly using BRAKER3 using IsoSeq data

annotate-braker3-with-bam

Annotate an assembly using BRAKER3 using a processed BAM file

annotate-genes-eggnog

Annotate genes using eggNOG

annotate-utrs-peaks2utr

Annotate an 3prime-UTRs using peaks2utr using a merged BAM file

assembly-check-contamination

Check for contamination in assembly using HiC data

atacseq-peaks-macs3

Generate peaks for bulk ATAC-Seq data using bwa and MACS3

correct-splice-variants-flair

Correct splice variants using flair

fastq-rRNA-filter

Filter rRNA reads from FASTQ files using SortMeRNA

fastq-rRNA-stats

Report the number of rRNA reads in FASTQ files

filter-model-vcf

Filter a model in resequencing VCF files using bcftools

filter-pops-vcf

Filter populations in resequencing VCF files using bcftools

filter-vcf

Filter resequencing VCF files using bcftools

hic-scaffolds-yahs

Scaffold an assembly with Hi-C data using YAHs

hifi-align-minimap2

Align hifi reseq reads to a genome assembly using minimap2

hifi-assemble-hifiasm

Assemble long reads using hifiasm and purge-dups

hifi-assemble-phased-hifiasm

Create phased assemblies from HiFi long reads using hifiasm

hifi-assembly-align-minimap2

Align hifi assemblies to a reference assembly for comparison using minimap2

hifi-assembly-purge-dups

Purge duplicate haplotigs from HiFi assemblies

hifi-assign-SVs-sniffles2

Assign structural variants to samples using Sniffles2

hifi-hic-assembly

Assemble long reads using hifiasm and scaffold with Hi-C data using yahs

iso-seq-align-minimap2

Align IsoSeq reads to a genome assembly using minimap2

mask-assembly

Mask an assembly using RepeatModeler

msa-phylogeny

Create a phylogenetic tree from multiple sequence alignments using IQ-TREE

msf-amino-acid-alignments

Create amino acid alignments using MUSCLE

msf-codon-alignments

Create codon alignments using MACSE

msf-codon-phylogeny

Create codon phylogenies by aligning with MACSE and trimming with ClipKIT

and then inferring trees with IQ-TREE

msf-codon-selection

Perform HyPhy selection analyses on MSFs by aligning with MACSE

trimming with ClipKIT

and inferring trees with IQ-TREE

process-egapx-annotations

Process eGAPx annotations

reseq-calc-nsl

Calculate nSL using selscan

reseq-calc-xpnsl

Calculate XP-nSL using selscan

reseq-gemma

Perform GWAS on resequencing data using GEMMA

reseq-popgen

Calculate Fst and perform a PCA on resequencing data using PLINK

reseq-unpruned-gemma

Perform GWAS on resequencing data using GEMMA with unpruned variants.

rnaseq-align-star

Align RNAseq reads within a genome assembly using STAR

rnaseq-counts-star

Count RNAseq reads within a genome assembly using STAR and featureCounts

rnaseq-splice-junctions

Align RNAseq reads within a genome assembly using STAR and extract splice junctions

seperate-pop-vcfs

Create separate VCF files for each population in a resequencing VCF file

tracking-naps

Track MP4 videos using SLEAP and NAPS

trim-fastqs

Trim short reads FASTQ files using fastp

trim-fcs-hifi-fastqs

Trim PacBio HiFi FASTQ files using HiFiAdapterFiltFSC

trim-fcs-hifi-pacbio

Trim PacBio HiFi BAMs using HiFiAdapterFiltFSC

trim-hifi-fastqs

Trim PacBio HiFi FASTQ files using HiFiAdapterFilt

trim-hifi-pacbio

Trim PacBio HiFi BAMs using HiFiAdapterFilt

unmapped-fastqs-star

Create unmapped FASTQs using STAR

Note

This table is automatically generated, please let us know if you find any errors or omissions using the pipemake GitHub.