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README.additional_info.md

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Additional information

1. List of workflow commands

Phylign is executed via GNU Make, which handles all parameters and passes them to Snakemake.

Here's a list of all implemented commands (to be executed as make {command}):

####################
# General commands #
####################
   all                Run everything (the default rule)
   help               Print help messages
   clean              Clean intermediate search files
   cleanall           Clean all generated and downloaded files
##################
# Pipeline steps #
##################
   conda              Create the conda environments
   match              Match queries using COBS (queries -> candidates)
   map                Map candidates to assemblies (candidates -> alignments)
#############
# Reporting #
#############
   config             Print configuration without comments
   report             Generate Snakemake report
###########
# Cluster #
###########
   cluster_slurm      Submit to a SLURM cluster
   cluster_lsf        Submit to LSF cluster
##################
# For developers #
##################
   format             Reformat Python and Snakemake files
   checkformat        Check source code format

Note: make format requires YAPF and Snakefmt, which can be installed by conda install -c conda-forge -c bioconda yapf snakefmt.

2. Directories

  • asms/, cobs/ Downloaded assemblies and COBS indexes
  • input/ Queries, to be provided within one or more FASTA/FASTQ files, possibly gzipped (.fa)
  • intermediate/ Intermediate files
    • 00_queries_preprocessed/ Preprocessed queries
    • 01_queries_merged/ Merged queries
    • 02_cobs_decompressed/ Decompressed COBS indexes (temporary, used only in the disk mode is used)
    • 03_match/ COBS matches
    • 04_filter/ Filtered candidates
    • 05_map/ Minimap2 alignments
  • logs/ Logs and benchmarks
  • output/ The resulting files (in a headerless SAM format)

3. File formats

Input files: FASTA or FASTQ files possibly compressed by gzipped. The files are searched in the input/ directory, as files with the following suffixes: .fa, .fasta, .fq, .fastq (possibly with .gz at the end).

Output files:

  • output/{name}.sam_summary.gz: output alignments in a headerless SAM format
  • output/{name}.sam_summary.stats: statistics about your computed alignments in TSV

SAM headers are omitted as all search experiments generate hits across large numbers of assemblies (many of them being spurious). As a result, SAM headers then dominate the outputs. Nevertheless, we note that, in principle, the SAM headers can always be recreated from the FASTA files in asms/, although this functionality is not currently implemented.

4. Known limitations

  • Swapping if the number of queries too high. If the number of queries is too high (e.g., 10M Illumina reads), the auxiliary Python scripts start to use too much memory, which may result in swapping. Try to keep the number of queries moderate and ideally their names short.
  • No support for ambiguous characters in queries. Queries are expected to be over the ACGT alphabet. All non-ACGT characters in queries are first converted to A.
  • Too many reported hits. When queries have too many equally good hits in the database, even if the threshold on the maximum number of hits is chosen low – for instance 10 – the program will take top 10 + ties, which can be a huge number (especially for short sequences).