wtpoa-cns polishing step

[crysclitheroe]

Dear @ruanjue !

Thank you for a great tool! I am trying to do the recommended polishing step with short read data, and Im wondering if the README polishing step can be clarified?

When I ran samtools as recommended and wtpoa-cns with the --x and --d param the programs quit by suggesting to look at the options.

I got them both to run by removing those options and trying:

samtools sort -T tmp_polish -o sr.srt.bam sr.bam samtools view sr.srt.bam | ./wtpoa-cns -t 8 -i prefix.ctg.fa -C 1 -fo prefix_polish.ctg.fa

But then nothing is in prefix_polish.ctg.fa.

Can you help with this?

Thanks and kind regards Crystal

[ruanjue]

Please use -x and -d instead of --x and '--d'.

[crysclitheroe]

Dear raunjue

My apologies this is what I meant, -x and -d. I am still getting the errors /work/BourguignonU/crystal/softwares/wtdbg2/wtpoa-cns: invalid option -- 'x'

I am missing something here; ./wtpoa-cns -t 16 -x sam-sr -d prefix.ctg.fa -i - -fo prefix.ctg.3rd.fa what is sam-sr, -d, and why is the input flag after the input in this case? also the solitary "-", what does that do?

Thanks and kind regards Crystal

[ruanjue]

To avoid discussing on different wtdbg2 version, please download the latest commit "https://github.com/ruanjue/wtdbg2/commit/3549831acf94382379e7855b8c7185b5643347b1".

-x sam-sr, -d prefix.ctg.fa. -i - means -i STDIN. - is often used for STDIN.

Jue

[crysclitheroe]

Thanks for the explanation, and I realize my version is out of date, so will update. But I am still confused about what is "sr-sam" some kind of file previously produced or a parameter argument?

[ruanjue]

$> wtpoa-cns -h
....
 -x <string> Presets, []
             sam-sr: polishs contigs from short reads mapping, accepts sorted SAM files
                     shorted for '-w 200 -j 150 -R 0 -b 1 -c 1 -N 50 -rS 2'

[crysclitheroe]

Thanks for freely sharing incredible software! I just finished my assemblies now they look amazing, even though you said your polishing tool is not as accurate. What other polishing tools would you suggest for higher accuracy?

[ruanjue]

Good polishers includes (not limit to) arrow/quiver, pilon, and nanopolish. I will find more time to improve wtpoa-cns, but not sure as well as them.

[mooym001]

I was wondering; has the -d option of wpoa-cns been removed? In the manual I read that polishing can be performed with samtools view -F0x900 dbg.bam | ./wtpoa-cns -t 16 -d dbg.raw.fa -i - -fo dbg.cns.fa but using the -d option gives an error for me, and asking for the wpoa-cns -h page only shows:

WTPOA-CNS: Consensuser for wtdbg using PO-MSA Author: Jue Ruan ruanjue@gmail.com Version: 1.1 Usage: wtpoa-cns [options] Options: -t Number of threads, [4] -i Input file(s) .ctg.lay from wtdbg, +, [STDIN] -o Output files, [STDOUT] -f Force overwrite -j Expected max length of node, or say the overlap length of two adjacent units in layout file, [1500] bp -M Match score, [2] -X Mismatch score, [-5] -I Insertion score, [-2] -D Deletion score, [-4] -B Bandwidth, [96] -W Window size in the middle of the first read for fast align remaining reads, [200] If $W is negative, will disable fast align, but use the abs($W) as Band align score cutoff -w Min size of aligned size in window, [$W 0.5] -A Abort TriPOA when any read cannot be fast aligned, then try POA -R Realignment bandwidth, 0: disable, [16] -C Min count of bases to call a consensus base, [3] -F Min frequency of non-gap bases to call a consensus base, [0.5] -N Max number of reads in PO-MSA [20] Keep in mind that I am not going to generate high accurate consensus sequences here -v Verbose

[ruanjue]

Maybe you were invoking very old version wtpoa-cns, wrong PATH?

WTPOA-CNS: Consensuser for wtdbg using PO-MSA
Author: Jue Ruan <ruanjue@gmail.com>
Version: 2.5 (20190621)
Usage: wtpoa-cns [options]
Options:
 -t <int>    Number of threads, [4]
 -d <string> Reference sequences for SAM input, will invoke sorted-SAM input mode
 -u <int>    XORed flags to handle SAM input. [0]
             0x1: Only process reference regions present in/between SAM alignments
             0x2: Don't fileter secondary/supplementary SAM records with flag (0x100 | 0x800)
...
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