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 |
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.