Home

Welcome to the screen_assembly wiki!

screen_assembly - last updated on 23rd March 2018

Screen a bacterial assemblies (contigs/CDS or proteins) for nucleotide or protein sequences.

Required dependencies: Blast, Muscle, common_modules/lab_modules.py (from my Github)

Optional dependencies: Raxml

Required arguments:

-q QUERY, –query QUERY

Query sequences fasta.

-i INPUT_FOLDER, –input_folder INPUT_FOLDER

Folder with ONLY db seqs in it. Can be one file or
many. Must be the same sequence type. Names of files and names of contigs with files will be used.
Do not use fullstops ('.') in file names, i.e., use sample_1.fa NOT sample.1.fa

optional arguments:

-h, --help            show this help message and exit
-t THREADS, --threads THREADS
                      How many threads to give blast, muscle, raxml etc.
-r, --raxml           Run raxml, requires alignments. Off by default.
-b BOOTSTRAPS, --bootstraps BOOTSTRAPS
                      Number of bootstraps for raxml. Default 100.
-m RAXML_MODEL, --raxml_model RAXML_MODEL
                      Model for raxml. Default is GTRGAMMA
-z RAXML_EXECUTABLE, --raxml_executable RAXML_EXECUTABLE
                      Default is raxmlHPC-PTHREADS-AVX2
-d, --dNdS            Calculate dNdS. Off by default.
-a, --aln             Make alignments with muscle. On by default.
-x, --plots           Make plots. On by default.
-pi, PERCENT_IDENTITY, --percent_identity PERCENT_IDENTITY
                      Percent_identity. Default 80.
-pl, PERCENT_LENGTH, --percent_length PERCENT_LENGTH
                      Percent_length. Default 80.
-o, --operon          Seq is operon or kmer, something where stops are
                      expected

Where a parameter is set to on/off by default use that flag to toggle the parameter to the opposite on/off.

Output:

Top level:

  blast_out.txt - raw blast output

  binary_hits.csv, total_hits.csv and hits_as_percentage.csv are the same thing except one is binary (presence absence), one is a count of hits and one reports the actual percentage of sequence identity of hits (biggest if more than one). Negative results are reported as 0, Ns (excluded due to high level of Ns), stops (excluded due to frame shift) and contigs (excluded due to hitting a contig break). The non zero negative hits are excluded from all plots but this DOES NOT mean they are not there.

  *_itol.txt - heatmap presence absence to drop into itol on tree (tree needs same samlpe names as used in contigs)

  sequence_variants.csv - the amount of different sequences for each gene screened.

  box_and_carriage_plot1.svg - high level summary of results. Shows carriage of genes and sequence variation between hits.

Per gene folder:

  *fa - various fasta files of the gene snipped from contigs

  *aln - various alignments

  *svg - various plots to show the point of variation