IMP3 input options

IMP3 is designed to perform integrated analyses of metaG and metaT data. Inputs can be either raw sequencing reads or already assembled contigs and mapped reads.

A typical workflow starts with a pair of files of paired-end metaG reads and a pair of metaT reads (both in FASTQ format, either gzipped or not). Alternatively, IMP3 can take only metaG or only metaT reads.

If the data is already assembled and the contigs should be annotated and binned into metagenomics-assembled genomes (MAGs), IMP3 also takes assemblies (in FASTA format) in addition to alignments (BAM files) or trimmed reads (FASTQ format) as input.

All inputs are defined in the config file.

Reads

The Metagenomics and Metatranscriptomics input fields expect two or three FASTQ or gzipped FASTQ files, separated by a space. The first two files should be the forward and reverse reads, if IMP3 analysis should start from pre-processing reads. The reads need to be in the same order in both files.

For processing the original raw Fastq files, the following setting should be used:

raws:
  Metagenomics: "/path/to/metagenomics.read.r1.fastq.gz /path/to/metagenomics.read.r2.fastq.gz"
  Metatranscriptomics: "/path/to/metatranscriptomics.read.r1.fastq.gz /path/to/metatranscriptomics.read.r2.fastq.gz"
  LongReads: ""
  LongReadTech: ""
  Contigs: ""
  Alignment_metagenomics: ""
  Alignment_metatranscriptomics: ""

If the user has already pre-processed reads, either for the Assembly step or for further analysis, the user is required to pass THREE files, two paired read files and one additional single ends file. The singleton read file is given last.

Note: In this case, the user should NOT include preprocessing in the IMP steps.

raws:
  Metagenomics: "/path/to/processed_metagenomics.read.r1.fastq.gz /path/to/processed_metagenomics.read.r2.fastq.gz /path/to/processed_metagenomics.read.se.fastq.gz"
  Metatranscriptomics: "/path/to/processed_metatranscriptomics.read.r1.fastq.gz /path/to/processed_metatranscriptomics.read.r2.fastq.gz /path/to/processed_metatranscriptomics.read.se.fastq.gz"
  LongReads: ""
  LongReadTech: ""
  Contigs: ""
  Alignment_metagenomics: ""
  Alignment_metatranscriptomics: ""

The user can also give only metaG or only metaT reads to IMP3, either raw or pre-processed.

If the user wishes to perform a metaG assembly including long reads, a single file of already pre-processed long-reads data (in Fastq format). In this case, additionally the sequencing method (possible values are nanopore and pacbio) can be added.

Note: The long reads are only used by IMP3, if metaspades is chosen as assembler.

raws:
  Metagenomics: "/path/to/metagenomics.read.r1.fastq.gz /path/to/metagenomics.read.r2.fastq.gz"
  Metatranscriptomics: ""
  LongReads: "/path/to/longread/reads.fastq"
  LongReadTech: ""
  Contigs: ""
  Alignment_metagenomics: ""
  Alignment_metatranscriptomics: ""

Contigs and alignments

If the user has already an assembly and would like to use IMP3 to annotate genes, perform binning and/or determine contig-level taxonomy, the contigs can be used as input in FASTA format (NOTE: the FASTA header should only contain the contig name, NO other information and NO spaces: >CONTIGNAME1). In addition, the user can give reads either in FASTQ files or already aligned as BAM files. For FASTQ files, the same limitations apply as discussed above. The BAM files should be sorted by contig name and coordinate, and again, the contig names are NOT allowed to contain spaces !!!).

raws:
  Metagenomics: ""
  Metatranscriptomics: ""
  LongReads: ""
  LongReadTech: ""
  Contigs: "/path/to/assembly.fasta"
  Alignment_metagenomics: "/path/to/metagenomics/read.sorted.alignment.bam"
  Alignment_metatranscriptomics: "/path/to/metatranscriptomics/read.sorted.alignment.bam"