Input reference¶

Short reads¶

Aviary accepts paired reads as separate forward and reverse lists (-1 and -2), interleaved reads (--interleaved), or a coupled list (--coupled). Choose one of these layouts; -1, --interleaved and --coupled are mutually exclusive.

reads/
├── sample_A_R1.fastq.gz
├── sample_A_R2.fastq.gz
├── sample_B_R1.fastq.gz
└── sample_B_R2.fastq.gz

When supplying lists to -1 and -2, keep samples in the same order. FASTQ files may be gzip-compressed. With multiple files, assembly behaviour depends on --coassemble; all supplied reads may still contribute differential coverage during genome recovery.

Paired listsInterleavedCoupled list

aviary complete \
  -1 sample_A_R1.fastq.gz sample_B_R1.fastq.gz \
  -2 sample_A_R2.fastq.gz sample_B_R2.fastq.gz

aviary complete --interleaved sample_A.interleaved.fastq.gz

aviary complete --coupled \
  sample_A_R1.fastq.gz sample_A_R2.fastq.gz \
  sample_B_R1.fastq.gz sample_B_R2.fastq.gz

Short-read identity option limitation

In the current parser, --min-percent-read-identity-short is in the same mutually exclusive group as -1, --interleaved and --coupled. Supplying it together with one of those inputs is rejected before the workflow starts. Its default remains 95; an explicit override is only accepted with input shapes that do not use those mutually exclusive flags.

Long reads¶

Supply one or more files with --longreads. --long-read-type accepts:

Value	Sequencing data
`ont`	Oxford Nanopore reads
`ont_hq`	high-quality/Q20 Oxford Nanopore reads
`rs`	PacBio RS II reads
`sq`	PacBio Sequel reads
`ccs`	PacBio CCS reads
`hifi`	PacBio HiFi reads

The default is ont. This selection affects parameters passed to upstream tools, so set it to the actual sequencing technology.

aviary assemble --longreads sample.nanopore.fastq.gz --long-read-type ont

Assemblies¶

--assembly accepts FASTA files containing scaffolded metagenome contigs. recover uses the supplied reads to calculate coverage. SemiBin2 multi-sample mode accepts multiple assemblies and requires --semibin-mode multi.

aviary recover --assembly week1.fasta week2.fasta week3.fasta \
  -1 week1_R1.fq.gz week2_R1.fq.gz week3_R1.fq.gz \
  -2 week1_R2.fq.gz week2_R2.fq.gz week3_R2.fq.gz \
  --semibin-mode multi

Genome collections¶

annotate reads FASTA files from --genome-fasta-directory. Use --fasta-extension when files do not use the default fna extension.

aviary annotate --genome-fasta-directory external_bins/ --fasta-extension fa

Previous Aviary runs¶

cluster --input-runs expects completed Aviary output directories containing the final-bin collection and bin summary needed for dereplication.

aviary cluster --input-runs runs/sample_A runs/sample_B runs/sample_C