Losing many contigs not reported in the contigs.reduced.fa.hetero.tsv file.

[Joseph Sevigny]

Hello,

I am very excited about redundans and I hope to use it consistently for all my projects ... if I can figure this out!

My unexpected results occur during the reduction phase of the pipeline. It seems that I am losing a bunch of content and losing all my smaller contigs.

Original Assembly QUAST results (contigs.fa)

# contigs (>= 0 bp)         46087

# contigs (>= 1000 bp)      23529

# contigs (>= 5000 bp)      11560

# contigs (>= 10000 bp)     6759

# contigs (>= 25000 bp)     1685

# contigs (>= 50000 bp)     221

After reduction (contigs.reduced.fa)

# contigs (>= 0 bp)         3907

# contigs (>= 1000 bp)      3907

# contigs (>= 5000 bp)      3907

# contigs (>= 10000 bp)     3907

# contigs (>= 25000 bp)     1685

# contigs (>= 50000 bp)     221

So it is basically removing all my contigs that have a length less than 10,000 regardless if they are duplicated. Only one contig  (~15,000 bp) shows up in the contigs.reduced.fa.hetero.tsv file.

Here are some BUSCO results showing the loss of content.

BUSCO original:

        554     Complete BUSCOs (C)

        504     Complete and single-copy BUSCOs (S)

        50      Complete and duplicated BUSCOs (D)

        118     Fragmented BUSCOs (F)

        306     Missing BUSCOs (M)

        978     Total BUSCO groups searched

BUSCO contigs.reduced.fa

        389     Complete BUSCOs (C)

        369     Complete and single-copy BUSCOs (S)

        20      Complete and duplicated BUSCOs (D)

        92      Fragmented BUSCOs (F)

        497     Missing BUSCOs (M)

        978     Total BUSCO groups searched

Switching around the options do not change this observations. Here is my typical run. 

redundans.py --identity 0.6 -i $forward $reverse -f $contigs -o redundans_out_60 -t 24

If it matters, I am currently working with a nematode that has ~150 MB genome and using illumina 250 bp reads. I am working with redundans-0.13c.

I appreciate any feedback.

Happy Holidays,

Joseph

[l.p.p...@gmail.com]

Hi Joseph,

This is peculiar. Can you send me Redundans log, and output of reduction (contigs.reduced.fa.hetero.tsv) and identity histogram (contigs.reduced.fa.hist.png)?

Bests,

L.

L.

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[Joseph Sevigny]

Than you for the quick reply. Attached are the files.

Thanks you.

- Joseph

L.

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[Joseph Sevigny]

Also, I can send you the raw contig file if you want to run it through on your end to rule out any dependency or hardware issues.. Just let me know the best secure way to send it.

- Joseph

On Tuesday, December 19, 2017 at 11:35:15 AM UTC-5, lpryszcz wrote:

L.

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[Joseph Sevigny]

Just wanted to give a quick update, While I still haven't found the cause, this observation seems to be isolated to this particular assembly.  The rest of my projects run as expected.

On Tuesday, December 19, 2017 at 11:35:15 AM UTC-5, lpryszcz wrote:

L.

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