prophyle / prophasm Goto Github PK

Great tool! I have a quick feature request. An option to output a presence/absence matrix or similar output would be very useful.

On a similar note, do you know of any software that would achieve this in a scalable manner for application to large prokaryotic datasets?

I am a little unclear on the recommended workflow for generating simplitigs from a bacterial pangenome.

As pangenomes aim to encompass all potential variants providing multiple input files via "-i" is probably unsuitable as the intersection would only include core K-mers (in all isolates). Is this correct? If that is the case, should the workflow be:

a) Concatenate all files (reads/assemblies separately) into a single fasta file and then process the concatenate with prophasm (might incur high memory overhead)

or

b) Compute simplitigs for each file and then concatenate the simplitig files together before running prophasm again? (lower memory usage)

Are there any other methodological considerations for these approaches that I have overlooked?

Thank you for your help,
Sion

You gave some functions implemented in python, the code looks incomplete, is it just an example you gave?

For cases, when too many -i/-o are provided

Apologies. This is a question I emailed to you, but it maybe of use to other users if posted here

I would be interested in generating simplitigs from fastq files. This raises a few questions:

1/ As ProPhasm does not accept fastq files would it be suitable to convert the reads directly to fasta or to k-mers before passing to ProPhasm?
2/ There are many potential sources of error/noise in raw reads so would you recommend pre-processing K-mers (filtering/correcting) before passing to ProPhasm?
3/ Would native frequency filtering be something you would consider instituting in the software?
4/ A K-mer size of 32 bp is the maximum allowed for the '-k' option. Could this be relaxed to allow for assembly with larger K-mers and how might this be achieved?

Thanks for your help!

            /usr/bin/time -v -o 23.fa.time prophasm -i GRCh38.fna -o 23.fa -k 23
            samtools faidx "23.fa"
        
=====================
1) Loading references
=====================
Loading GRCh38.fna
===============
2) Intersecting
===============
-1961571780 -1961571780 ...inter:0
=============
3) Assembling
=============
   assembly finished (16655985 contigs)
[E::fai_build_core] Format error, unexpected "C" at line 200497
[faidx] Could not build fai index 23.fa.fai
[Tue Aug 13 16:28:25 2019]
Error in rule 2:
    jobid: 0
    output: 23.fa
    shell:
:

Memory estimates:

       Command being timed: "prophasm -i GRCh38.fna -o 23.fa -k 23"
        User time (seconds): 5738.61
        System time (seconds): 1615.14
        Percent of CPU this job got: 99%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 2:03:11
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 93147084
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 6
        Minor (reclaiming a frame) page faults: 1879671766
        Voluntary context switches: 33101
        Involuntary context switches: 42593
        Swaps: 0
        File system inputs: 6451232
        File system outputs: 5712856
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0