ATAC-seq: a step-by-step analysis pipeline.

UNDER CONSTRUCTION

A step-by-step pipeline for the analysis of ATAC-seq data (the assay for transposase-accessible chromatin with sequencing), written by the Cebola Lab. The resources used to build this pipeiline are listed at the bottom in the Resources section.

Correspondence = hannah.maude12@imperial.ac.uk

The following steps will be covered:

Pre-alignment processing

Pre-alignment quality control (QC): QC reports and adapter trimming

Alignment, QC and track visualisation

Alignment
Post-alignment QC: filter, check library complexity and format for peak calling
Bam visualisation, bam to bigWig: generate tracks to visualise the aligned data on a genome browser

Peak calling, QC and visualisation

Peak calling: call peaks using MACS2, HMMRATAC and Genrich
Peak calling QC: FRiP, transcription start site enrichment, sample reproducibility
Peak visualisation: p-value, peaks and pileup

Differential accessibility analysis

Differential accessibility (DA) analysis
Functional analysis & Motif Discovery

Pre-alignment QC

Independent replicates should be processed separately.

Initial QC report

The raw sequence data should first be assessed for quality. FastQC reports can be generated for all samples to assess sequence quality, GC content, duplication rates, length distribution, K-mer content and adapter contamination. In ATAC-seq data, it is likely that Nextera sequencing adapters will be over-represented. As described by Yan et al. (2020), base quality should be high although may drop slightly at the 3' end, while GC content and read length should be consistent with the expected values. For paired-end reads, run fastqc on both files, with the results output to the current directory:

fastqc <sample>_R1.fastq.gz -d . -o .

fastqc <sample>_R2.fastq.gz -d . -o .

Adapter trimming

Adapters and low quality reads/bases should be trimmed using one of several programs, such as trimmomatic, cutadapt, or fastp. Adapter contamination can be seen in the fastqc report:

For this pipeline, fastp is used to remove adapter sequences.

fastp -i <sample>_R1.fastq.gz -I <sample>_R2.fastq.gz -o <sample>_R1.trimmed.fastq.gz -O <sample>_R2.trimmed.fastq.gz --detect_adapter_for_pe -j <sample>.fastp.json -h <sample>.fastp.html

The output of fastp includes a html report, part of which is shown below. This presents the total number of reads before and after filtering, including the % of high quality (Q30) bases. The report also shows the main causes of read removal. In the example below, 1.9% of reads were removed because they were shorter than the minimum read length specified above by the -l argument (25bp).

Alignment

The processed reads should then be aligned to the reference human genome using an aligner such as bowtie2. This pipeline will use bowtie2 to align reads to the hg19 reference genome. If the user is aligning to the more recent GRCh38 release, it is recommended to remove alternative contigs, otherwise reads may not map uniquely and will be assigned a low quality score. Suggested guidelines for preparing the GRCh38 genome are discussed in this tutorial. If the user selects an alternative alignment tool, such as bwa, they are referred to this blog post which discusses the resulting differences in alignment quality scores.

Bowtie2 alignment

The local parameter is used to 'soft clip' the end of reads to allow the best possible alignment, including any remaining adapter sequences (e.g. 1 or 2bp). By using the --no-mixed and --no-discordant parameters, reads will only be aligned if both reads align successfully as a pair (this avoids the need to later remove reads which are not properly paired, which is a common post-alignment QC step). The -I 25 and -X 700 require fragments to be greater than 25bp and less than 700bp. The user can adjust these depending on the experiment/sequencing protocol (see the fastp html report for a plot of the estimated insert sizes). The maximum fragment length of 700bp prevents reads from aligning incorrectly outside the expected fragment range.

Which reference genome to use? See this discussion on which reference genome to use. The recommended downloads for both hg19/b37 and GRCh38 are shown below.

#to download the build 37 (hg19) reference genome
wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz

#to download the more recent GRCh38
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

#Remember to extract the files using gunzip!

Bowtie2 should be used to create the reference genome index files (see the bowtie2 manual). After the index files have been generated, align the trimmed ATAC-seq fastq files to the genome:

#set the bt2idx variable to the directory with the reference genome and indexes
bt2idx=/path/to/reference-genome

IMPORTANT: if your sample has been sequenced across multiple lanes, these files can be combined in the bowtie command. The -1 and -2 arguments can accept a comma-seperated list of files.

To align to hg19/b37:

#Run the bowtie2 alignment and output a bam alignment file
bowtie2 --local --very-sensitive --no-mixed --no-discordant -X 700 -x $bt2idx/human_g1k_v37 -1 <sample>_R1.trimmed.fastq.gz -2 <sample>_R2.trimmed.fastq.gz | samtools view -bS - > <sample>.bam

To align to GRCh38:

bowtie2 --local --very-sensitive --no-mixed --no-discordant -I 25 -X 700 -x $bt2idx/GCA_000001405.15_GRCh38_no_alt_analysis_set -1 <sample>_R1.trimmed.fastq.gz -2 <sample>_R2.trimmed.fastq.gz | samtools view -bS - > <sample>.bam

The output bam file should be sorted and indexed prior to the downstream analysis:

#Sort the output bam file by coordinate
samtools sort <sample>.bam -o <sample>_sorted.bam 

#Generate an index file
samtools index <sample>_sorted.bam

Post-alignment QC

The post-alignment QC involves several steps:

Remove mitochondrial reads
Remove duplicates & low-quality alignments (including non-uniquely mapped reads)
Calculate library complexity and QC
Remove ENCODE blacklist regions
Shift read coordinates

For an ATAC-seq experiment, the number of uniquely mapped reads after these steps is recommended to be 25 million for single-end or 50 million paired-end reads (Buenrostro et al. 2015). Specific to ATAC-seq, an additional QC step is to check the fragment size distribution, which is expected to correspond to the length of nucleosomes:

Assess fragment size distribution

Remove mitochondrial reads

ATAC-seq experiments commonly include a high proportion of mitochondrial reads. These should be removed. To assess the total % of mitochondrial reads, samtools idxstats can be run to report the total number of reads mapped to each chromosome. samtools flagstat provides a short report including the total number of DNA reads as the first line (halve this number for the total number of fragments).

#Generate the idxstats report
samtools idxstats <sample>_sorted.bam > <sample>_sorted.idxstats

#Check the number of reads mapped to the mitochondria (chrM)
grep "chrM" <sample>_sorted.idxstats

The second column is the length of the chromosome and the third column is the total number of reads aligned to the chromosome (chrM). To see the total number of DNA fragments, run:

#Generate the flagstat report
samtools flagstat <sample>_sorted.bam > <sample>_sorted.flagstat

#check the total number of aligned fragments
head <sample>_sorted.flagstat

The % of DNA fragments aligned to chrM can be calculated as a % of the total DNA fragments. To remove any mitocondrial DNA, run the following:

#Remove reads aligned to the mitochondria
samtools view -h <sample>_sorted.bam | grep -v chrM | samtools sort -O bam -o <sample>.rmChrM.bam -T .

Mark duplicates

To mark duplicate reads and view the % of duplicates:

picard MarkDuplicates QUIET=true INPUT=<sample>.rmChrM.bam OUTPUT=<sample>.marked.bam METRICS_FILE=<sample>.dup.metrics REMOVE_DUPLICATES=false CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT TMP_DIR=.

#View the % of duplicates
head -n 8 <sample>.dup.metrics | cut -f 7,9 | grep -v ^# | tail -n 2

Remove duplicates & low-quality alignments

The output sam/bam files contain several measures of quality. First, the alignment quality score. Reads which are uniquely mapped are assigned a high alignment quality score and one genomic position. If reads can map to more than one location, Bowtie2 reports one position and assigns a low quality score. The proportion of uniquely mapped reads can be assessed. In general, >70% uniquely mapped reads is expected, while <50% may be a cause for concern (Bailey et al. 2013). Secondly, the 'flag' reports information such as whether the read is mapped as a pair or is a PCR duplicate. The individual flags are reported here and are combined in a sam/bam file to one score, which can be deconstructed back to the original flags using online interpretation tools. In this pipeline, the bowtie2 parameters --no-mixed and --no-discordant prevent the mapping of only one read in a pair, so these flags will not be present. All flags reported in a sam file can optionally be viewed using grep -v ^@ <sample>.sam | cut -f 2 | sort | uniq.

Multi-mapping: the user should decide whether or not to retain reads which have multi-mapped, i.e. aligned to more than one position in the reference genome. When using paired-end data, it may be the case that one read aligns to a repetitive region (and therefore can map elsewhere), while the mate aligns to a unique sequence with a high quality. The bowtie2 parameters used above required reads to align within 50-700bp, so there should be no reads incorrectly aligned outside this distance. As such, the user may decide to keep multi-mapping reads on the assumption that they are likely to be mapped to the correct sequence, within the length of the DNA fragment. This may, however, cause incorrect alignments in extended repetitive regions where a read could map to multiple positions within the length of the DNA fragment. This should be minimised by the downstream removal of the ENCODE Blacklisted regions.

If a read is multi-mapped, it is assigned a low quality score by bowtie2. To view how many DNA reads align with a quality score >30, run the following (divide this number by 2 to calculate the # of DNA fragments):

samtools view -q 30 -c <sample>.marked.bam

A low % of uniquely mapped reads map result from short reads, excessive PCR amplification or problems with the PCR (Bailey et al. 2013). The following code uses the sam/bam flags to retain properly mapped pairs (-f 2) and to remove reads which fail the platform/vendor QC checks (-F 512), duplicate reads (-F 1024) and those which are unmapped (-F 12). The three flags to be removed can be combined into -F 1548, which will remove reads which meet any of the three individual flags

Here we will remove multi-mapped reads:

samtools view -h -b -f 2 -F 1548 -q 30 <sample>.marked.bam | samtools sort -o <sample>.filtered.bam

samtools index <sample>.filtered.bam

#To retain multi-mapped reads:
#samtools view -h -b -f 2 -F 1548 <sample>.rmChrM.bam | samtools sort -n -o <sample>.filtered.bam

Remove ENCODE blacklist regions

The ENCODE blacklist regions, most recently reported by Amemiya et al. (2019) are defined as 'a comprehensive set of regions in the human, mouse, worm, and fly genomes that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment.' These problematic regions should be removed before further analysis. Download the blacklist files for your chosen reference genome from the Boyle Lab github repository. Details regarding the identification of blacklist regions are reported here.

#Remove reads within the blacklist regions
bedtools intersect -nonamecheck -v -abam <sample>.filtered.bam -b hg19-blacklist.v2.bed > <sample>.tmp.bam

#Sort and index the bam file
samtools sort -O bam -o <sample>.blacklist-filtered.bam <sample>.tmp.bam
samtools index <sample>.blacklist-filtered.bam

rm <sample>.tmp.bam

Shift read coordinates

An optional step in analysing data generated using the Tn5 transposase (such as ATAC-seq, ChIPmentation etc.) is to account for a small DNA insertion, introducted as repair of the transposase-induced nick introduces a 9bp insertion. Reads aligning to the + strand should be offset by +4bp and reads aligned to the -ve strand should be offset by -5bp. For references, see the first ATAC-seq paper by Buenrostro et al., (2013) and the analysis by Adey et al., (2010) which showed this insertion bias. Shifting coordinates is only really important if single-base resolution is required, for example in the analysis of transcription factor motifs in ATAC-seq peak footprints. Be aware that some tools do this shifting themselves (so double check manuals!).

We can use the deeptools package.

alignmentSieve --numberOfProcessors max --ATACshift --blackListFileName hg38-blacklist.v2.bed --bam blacklist-filtered.bam -o ${prefix}.shifted.bam

# samtools index ${prefix}.shifted.bam

Assess fragment size distribution and QC

The fragment size is expected to show a periodicity of 150/200 bp, reflecting the length of DNA surrounding nucleosomes, since the tagmentation typically cuts DNA in between nucleosomes. The R tool ATACseqQC can be used to assess the distribution of fragments. Fragments sizes may also be <100bp, corresponding to nucleosome-free regions or cutting of linker DNA, as well as fragments of and mono-, di-, and tri-nucleosomes (~200, 400 and 600bp, respectively) (Yan et al. 2020). Fragments from nucleosome-free regions are expected to be enriched around transcription-start sites (TSS) and fragments from nucleosome-bound regions are depleted around TSS and maybe be slightly enriched in the flanking regions. The ATACseqQC manual is available here.

Estimate library complexity
Fragment size distribution
GC bias
Nucleosome positioning
Plot footprints
Plot correlations between samples

The <sample>.shifted.bam file should be analysed in the following steps.

TO BE COMPLETED

Bam visualisation

Through this pipeline, two types of tracks will be generated for visualisation in genome browsers. The first, generated here, will show the aligned reads and are generated from the processed bam file. The second, generated after peak calling, will show the -log₁₀ p-value from the peak calling.

The deeptools command bamCoverage will be used. The input to bamCoverage (see below) requires the effective genome size to be estimated; a table is provided at this link. Select the appropriate value depending on the read length and reference genome.

#2862010578 is the effective genome size for GRCh38 when using 150bp reads and including only regions which are uniquely mappable
# bam to bigwig
# Set your preferred number of processors
bamCoverage --numberOfProcessors 8 --binSize 10 --normalizeUsing BPM \
  --effectiveGenomeSize 2862010578 --bam <sample>.shifted.bam -o <sample>_coverage_BPM.bw

Peak calling

Peaks are identified where sequenced reads accumulate. These correspond to regions of accessible DNA.

In this pipeline, peaks will be called using several alternative software: MACS2, HMMRATAC, developed by Tarbell et al. (2019) and the popular but unpublished Genrich. While MACS2 is the most popular peak caller and may be used to generate results consistent with other published data, Yan et al. (2020) recommend using the peak caller HMMRATAC, developed by Tarbell et al. (2019), which is specifically developed for ATAC-seq data (if computational resources are sufficient). HMMRATAC is available on github. Genrich also has a dedicated ATAC-seq mode and is particularly popular as many QC steps are built in. First, MACS2 will be used to call peaks.

Important considerations for ATAC-seq:

There are usually no controls
The Tn5 transposase has a binding preference, resulting in a GC bias which should be corrected for during peak calling
Repair of the transposase-induced nick introduces a 9bp insertion (completed above).

Peak calling - MACS2

The following steps will be carried out:

Call peaks for individual replicates
Call replicated peaks for the pooled replicates
Call 'high-confidence' IDR peaks.

If using paired-end reads, MACS2 will be used with the -f BEDPE option. Depending on the analysis aims, there are several different options that can be used. The ENCODE3 pipeline uses the --nomodel --shift -37 --extsize 73 options for analysing ATAC-seq data, to account for the size of nucleosomes. Nucleosomes cover ~145 bp and the ATAC-seq reads need to be shifted towards the 5' end by half this distance.

#Convert the bam file to BEDPE
macs2 randsample -i <sample>.shifted.bam -f BAMPE -p 100 -o <sample>.bed

#Call peaks
macs2 callpeak -f BEDPE --nomodel --shift -37 --extsize 73 -g 2862010578 -B --broad --keep-dup all --cutoff-analysis -n <sample> -t <sample>.bed --outdir macs2/<sample> 2> macs2.log

The output files:

_broad_treat_pileup.bdg: bedGraph format for the treatment sample
_broad_control_lambda.bdg: bedGraph format for the background note
_broad_peaks.broadPeak: a BED6+4 file detailing the peak locations, along with the peak summits, p-value and q-values
_broad_peaks.gappedPeak
_broad_peaks.xls: a tabular file containing addition information, such as pileup and fold-enrichment.

Output file: the <sample>_broad_peaks.broadPeak is a bed file containing the peak information for the INDIVIDUAL replicate*.

*The <sample>_peaks.broadPeak can be uploaded and visualised via a genome browser such as UCSC. The bed file of peak calls is referred to at this stage as 'relaxed' peak calls, since they are called for individual replicates. Two or more biological replicates will be combined in the next stage to generate a combined set of peaks.

The total number of peaks can be obtained using wc -l <sample>_peaks.broadPeak.

QC value: input the total number of peaks into the QC spreadsheet.

From these output files, we will generate:

A bigWig track of the fold-enrichment (treatment over the background)
A bigWig track of the -log₁₀ p-value (treatment over the background)

1. Fold-enrichment bigWig

The following commands require an input file detailing the chromosome sizes. Use the UCSC tool fetchChromSizes (install via conda): fetchChromSizes hg38 > hg38.chrom.sizes. Conda can also be used to install conda install -c bioconda ucsc-bedgraphtobigwig.

#Generate the fold-change bedGraph
macs2 bdgcmp -t <sample>.broad_treat_pileup.bdg -c <sample>.broad_control_lambda.bdg -m FE -o <sample>_FE.bdg 

#Sort the bedGraph file and convert to bigWig
sort -k1,1 -k2,2n <sample>_FE.bdg > <sample>_FE.sorted.bdg

bedGraphToBigWig <sample>_FE.sorted.bdg hg38.chrom.sizes <sample>_macs2_FE.bw

Output file: <sample>_macs2_FE.bw

2. -log₁₀ p-value bigWig

#Generate the p-value bedGraph
macs2 bdgcmp -t <sample>.broad_treat_pileup.bdg -c <sample>.broad_control_lambda.bdg -m ppois -o <sample>_ppois.bdg

#Sort the bedGraph file and convert to bigWig
sort -k1,1 -k2,2n <sample>_ppois.bdg > <sample>_ppois.sorted.bdg

bedGraphToBigWig <sample>_ppois.sorted.bdg hg38.chrom.sizes <sample>_macs2_pval.bw

Output file: <sample>_macs2_pval.bw

The <sample>_macs2_pval.bw and <sample>_macs2_FE.bw output files can visualised in a genome browser, such as UCSC.

QC - fraction of reads in peak (FRiP score)

One quality metric for peak calling is to calculate the fraction of reads in peak (FRiP) score. For ATAC-seq, the FRiP score is recommended to be >0.2, with >0.3 as optimal. We will use featureCounts from the SourceForge Subread package. Install Subread using conda install -c bioconda subread (or see this link to install from the source).

### covert BED (the peaks) to SAF
awk 'BEGIN{FS=OFS="\t"; print "GeneID\tChr\tStart\tEnd\tStrand"}{print $4, $1, $2+1, $3, "."}' <sample>_peaks.broadPeak > <sample>_peaks.saf

### count
featureCounts -p -a <sample>_peaks.saf -F SAF -o <sample>-readCountInPeaks.txt <sample>.shifted.bam

QC value: input the FRiP score into the QC spreadsheet.

Call peaks for pooled replicates

The step assumes that the ATAC-seq expriment includes biological replicates for each treated condition. Best practise requires a combined set of peaks for the pooled replicates to be called. The following code assumes that there are two biological replicates, rep1 and rep2, but the same can be run for any number of replicates.

First, check the correlation between the replicates using the UCSC tool wigCorrelate (conda install -c bioconda ucsc-wigCorrelate):

wigCorrelate <sample>_rep1_macs2_FE.bw <sample>_rep2_macs2_FE.bw

Assuming there is a satisfactory correlation, call peaks on the combined replicates by including all the files in the macs2 callpeak command. First, ensure all samples have been converted to BEDPE format using macs2 randsample.

#call peaks
macs2 callpeak -q 0.01 -f BEDPE --nomodel --shift -37 --extsize 73 -B --broad -g 2862010578 --keep-dup all --cutoff-analysis -n <sample>_pooled -t <sample>_rep1.bed <sample>_rep2.bed --outdir macs2/<sample>_pooled 2> macs2_<sample>_pooled.log

Output file: <sample>_pooled_broad_peaks.broadPeak

Extract replicated peaks

The following code is adapted from the ENCODE pipeline.

Replicated peaks are defined by ENCODE as peaks present in the pooled analysis, as well as in both replicates. ENCODE require replicated peaks to overlap by at least 50% for either of the two peaks. First, the pooled peaks will be subsetted for those which overlap replicate 1, then further subsetted for those which also overlap replicate 2.

#For BROAD peaks.
#Identify peaks from the POOLED replicates which are in BOTH replicate 1 and replicate 2

#First extract pooled peaks which are in replicate 1
intersectBed -wo -a <sample>_pooled.broadPeak -b <sample>_rep1_peaks.broadPeak  | awk 'BEGIN {FS="\t" ; OFS = "\t"} {s1=$3-$2 ; s2=$12-$11; if(($19/s1 > 0.5) || ($19/s2 > 0.5)) {print $0}}' | cut -f 1-9 > tmp.bed

#Next, take these peaks and extract the ones which also overlap with replicate 2
intersectBed -wo -a tmp.bed -b <sample>_rep2_peaks.broadPeak | awk 'BEGIN {FS="\t" ; OFS = "\t"} {s1=$3-$2 ; s2=$12-$11; if(($19/s1 > 0.5) || ($19/s2 > 0.5)) {print $0}}' | cut -f 1-9 > <sample>.replicated_broadPeak.bed

Output file: <sample>.replicated_broadPeak.bed

The number of peaks within a replicated peak file should be >150,000, though values >100,000 may be acceptable. Check this using wc -l.

STOP HERE

HMMRATAC

If working with a Conda environment, HMMRATAC can be installed using conda install -c bioconda hmmratac (check the releases to make sure there is not a more recent version, in which case download the executable file and run hmmratac directly).

samtools view -H <sample>.shifted.bam | perl -ne 'if(/^@SQ.*?SN:(\w+)\s+LN:(\d+)/){print $1,"\t",$2,"\n"}' > genome.info

HMMRATAC -b <sample>.shifted.bam -i <sample>.shifted.bam.bai -g genome.info -o <sample>

#java -jar HMMRATAC_V1.2.10_exe.jar -b <sample>.filtered.bam -i <sample>.filtered.bam.bai -g genome.info -o <sample>

The output files:

Genrich

See this post from Harvard FAS Informatics. Genrich does everything in one go!

Other peak callers

NucleoATAC ?

... check reproducibility of peaks between replicates... then re-run MACS2 with the merged bam file.

Peak QC

Quality control steps should be carried out to assess the called peaks, as well as reproducibility between samples.

Quality control of the peaks, along with differential accessiblity analysis (if this is an aim of your project) will be carried out.

The following analysis will be completed in R

See ENCODE ATAC-seq data standards and prototype processing pipeline

The number of peaks
Fraction of reads in peaks (FRiP) score
Transcription start site (TSS) enrichment
Biological replicate peak overlap
Compare normalisation methods and systematic biases

Number of peaks should be >150,000 and not less than 100,000 (>70,000 in an IDR file)

Differential accessibility

Yan et al. (2020) recommendations for ATAC-seq data analysis: csaw for peak differential analysis ChIPseeker for annotation and visualisation MEME suite for motic detection and enrichment HMMRATAC for nucleosome detection HINT-ATAC for footprint analysis PCEA for regulatory network reconstruction with RNA-seq HOMER for motif discovery.

TSS enrichment should be ideally >10 for hg19 and not <6 and ideally >7 and not <5 for GRCh38.

HOMER can be used for genomic annotation.

FRiP score should be >0.3 and not less than 0.2.

Biological replicate peak overlap: ENCODE-define naive overlap which calls peaks on pooled replicates and then identifies peaks with >50% overlap with all single replicate peaks.

Visualisation

The QC-ed bam file can be converted to a bedGraph format to visualise sequencing trakcs using tools such as the UCSC browser or the integrative genomes browser. The ENCODE blacklist regions can be provided, to exclude them from the output:

bedtools bamCoverage --normalizeUsing BPM -b <sample>.filtered.bam > <sample>.bedGraph

TmpScale=$(bc <<< "scale=6;1000000/$(samtools view -f 0 -c mybamfile.bam)") bedtools genomecov -ibam mybamfile.bam -bg -scale $TmpScale -g mm10.chrom.sizes > myBedGraphfile.BedGraph

The -bg option can be replaced with -bga if the user wants the output file to contain regions with 0 coverage.

Additional analysis: motif calling

An important step with ATAC-seq data is to shift reads +4bp and -5bp for positive and negative strands, due to the 9bp duplication introducted through the repair of the Tn5 transposase nick.

A recent tool which can be used to assess motifs and transcription factor footprints is TOBIAS.

picard CollectInsertSizeMetrics

Resources

This pipeline has been developed using guidance from the following resources:

https://vallierlab.wixsite.com/pipelines/atac-seq A great tool for beginners indicating the major analysis steps
https://www.encodeproject.org/atac-seq/ The recommended ENCODE pipeline, for which tools are available on github and the recommended parameters/specification are available via a google doc
https://github.com/harvardinformatics/ATAC-seq An ATAC-seq pipeline from Harvard Informatics
https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/ A similar github page presenting an ATAC-seq pipeline
https://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html
Standardized ENCODE pipeline devides by Kundaje et al. https://libraries.io/github/kundajelab/atac_dnase_pipelines
Hbctaining tutorial for peak calling

An recent review on the ATAC-seq analysis pipeline is reported by Yan et al. (2020).

hengbingao / ATAC-seq