Module Input Input Format Output Output File Names
sample_reads FASTQ file(s) .fastq.gz or
.fastq or
.fq		 Subampled FASTQ file(s) sample_1.fastq
sample_2.fastq
trim_reads FASTQ file(s) .fastq.gz or
.fastq or
.fq		 Trimmed FASTQ file(s) and
summary from Trimmomatic text file		 trimmed_1.fastq
trimmed_2.fastq
trimmed_U.fastq
trimmomatic_summary.out
join_reads FASTQ file(s) .fastq.gz or
.fastq or
.fq		 FASTQ files for joined reads and unjoined reads joined.fastq
notjoined_1.fastq
notjoined_2.fastq
ec_reads FASTQ file(s) .fastq.gz or
.fastq or
.fq		 Error corrected FASTQ file(s) corrected_1.fastq
corrected_2.fastq
corrected_U.fastq
assemble_denovo FASTQ file(s) .fastq.gz or
.fastq or
.fq		 De novo assembled contigs FASTA file and
de novo summary text file		 denovo_contigs.fna
denovo_summary.txt
assemble_amplicons FASTA files and
GTF file		 .fna or
.fasta or
.fa and
.gtf		 FASTA file with assembled amplicons amplicon_assembly.fna
assemble_scaffold FASTA files .fna or
.fasta or
.fa		 FASTA files with scaffolded and aligned sequences and
FASTA file with assembled amplicons		 scaffold_aligned.fa
scaffold_assembly.fa
scaffold_imputed.fa
scaffold_padded.out
align_reads FASTQ files and
FASTA file		 .fastq.gz or
.fastq or
.fq and
.fna or
.fasta or
.fa		 Aligned BAM file and
Bowtie2 alignment output summary text file		 aligned.bam
aligned.bt2.out
call_variants BAM and
FASTA file		 .bam and
.fna or
.fasta or
.fa		 VCF file with variants variants.vcf.gz
vcf_to_consensus VCF file .vcf FASTA file with consensus sequence consensus.fna
refine_assembly FASTQ files and
FASTA file		 .fastq.gz or
.fastq or
.fq and
.fna or
.fasta or
.fa		 FASTA file with refined consensus sequence refined.fna
finalize_assembly FASTQ files and
FASTA file		 .fastq.gz or
.fastq or
.fq and
.fna or
.fasta or
.fa		 FASTA file with final refined consensus sequence and
final BAM file with reads aligned to final FASTA file and
VCF file with variants relative to final.fna		 final.fna and
final.bam and
final.vcf.gz
predict_haplo FASTQ files and
FASTA file		 .fastq.gz or
.fastq or
.fq and
.fna or
.fasta or
.fa		 PredictHaplo's fasta-like output file best.fa
ph_parser PredictHaplo's FAS output file .fas Summary text file with haplotype diversity statistics and
FASTA file with haplotype sequences		 ph_summary.txt and
ph_haplotypes.fna
clique_snv FASTQ files and
FASTA file		 .fastq.gz or
.fastq or
.fq and
.fna or
.fasta or
.fa		 FASTA file with haplotype sequences and TXT files with summary information cs0X_REGION.fasta
cs0X_REGION.txt
cs0X_REGION_summary.txt
pairwise_align FASTA files and
GTF file		 .fna or
.fasta or
.fa and
.gtf		 JSON file pairwise_aligned.json
extract_pairwise JSON file from pairwise_align output .json FASTA output with region extracted to standard out stdout.fasta
summary_stats Direcoty lists for assembly and haplotype files (TXT) .txt Summary statistics (TXT and TSV) summary_stats.txt
summary_stats.tsv
PH_summary_stats.tsv
multiple_align FASTA files and/or
directory list (TXT)
and GTF file		 .fna or
.fasta or
.fa and .txt
and
.gtf		 FASTA alignment and sequence files separated by amplicons in GTF alignment_regionX.fasta
all_sequences_regionX.fasta
model_test FASTA or PHYLIP alignment file .fna or
.fasta or
.fa or
.phy		 Text file containing best-fit models modeltest_results.out
build_tree FASTA or PHYLIP alignment file .fna or
.fasta or
.fa		 RAxML output files RaxML_info.build_tree.tre and RAxML tree files