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Module Specification

Assembly

  • Version: 0.2.0

Output:

Assembly file names must fulfill the following name pattern:

SAMPLENAME_contigs.fa.gz

Contig names must be renamed according to the following pattern:

SAMPLEID_SEQUENCECOUNTER_SEQUENCEHASH

where

  • SAMPLEID is the name of the dataset (e.g: SRR234235)

  • SEQUENCECOUNTER is the counter of the contig entry in the fasta file (e.g: 2)

  • SEQUENCEHASH are the last 5 characters of an md5sum hash of the fasta entry without the header and newline character. (eg. echo -n "ACGT" | md5sum | cut -d ' ' -f 1 | cut -c -5 )

Binning

  • Version: 0.5.0

Output:

Binning file names must fulfill the following name pattern:

SAMPLENAME_bin.NUMBER.fa

Where NUMBER is a unique identifier per SAMPLE.

Contig names must be renamed according to the following pattern:

SAMPLEID_SEQUENCECOUNTER_SEQUENCEHASH MAG=BINNUMBER

where

  • SAMPLEID, SEQUENCECOUNTER and SEQUENCEHASH definitions can be inspected in the assembly specification.

  • BINNUMBER is an unique identifier per SAMPLE.

MAG Attributes

  • Version: 0.1.0

Output:

SAMPLENAME_TOOLNAME_CHUNK.tsv

where * TOOLNAME could be for example checkm, gtdb etc. * CHUNK is a random identifier that produces values for one part of all MAGs of a given sample.

FORMAT

The header line specifies the following columns: 

BIN_ID  SAMPLE  BIN_ATTRIBUTE1  BIN_ATTRIBUTE2 ...

where * BIN_ID is unique for the samples. * BIN_ATTRIBUTES All column names that are not BIN_ID or SAMPLE can be any property of a MAG, like contamination, completeness etc.

Quality Control

  • Version: 0.1.0

Output:

SAMPLE_interleaved.qc.fq.gz