Andean condor Project

--- title: 'Andean condor Project' --- *Pehuel* Genome Assembly === ###### tags: `Condor Project` It is a captive male Andean condor used as a primary genetic founder in the breeding program of the Buenos Aires Zoo. The approx. 65 years-old individual was originally from the Andean province of Mendoza (Argentina), a region encompassing the highest mountains in the Americas (up to 6.961 masl). ### Available Data * WGS: 1 lane HiSeq 4000 2x151bp (75,14 Gbp) * ONT: 2 MinION runs (2,39 Gbp) * HiC: 1 lane HiSeq 2000v4 2x76bp (30,27 Gbp) ## QC and trimming |Sample|Length (bp)|M Seqs| |-|:-:|:-:| |WGS.a.1|151|55.4| |WGS.a.2|151|55.4| |WGS.b.1|151|193.4| |WGS.b.2|151|193.4| |ONT|13436|0.3| |HiC.1|76|199.2| |HiC.2|76|199.2| :scissors: Post demito mapping and trimming |Sample|Length (bp)|M Seqs| |-|:-:|:-:| |WGS.1|150|246.3| |WGS.2|147|246.3| |ONT|13437|0.3| |HiC.1|75|198.3| |HiC.2|75|198.3| :::info Quality of the WGS and HiC reads is OK. ONT sequencing was **very** low throughput. ::: --- ![](https://i.imgur.com/jGXopnG.png) ```csvpreview {header="false"} Estimated genome size,1 315 114 606 bp Transition parameter*,33 Maximum read depth,99 ``` *transition between haploid and diploid coverage depths :::success Genome size estimation is reasonable. The heterogeneity is low. ::: [Assembly pipeline](https://github.com/diegomics/Pahuel_assembly_pipeline) === ![](https://i.imgur.com/s9k3Ime.png) MaSuRCA assembly & purge_dups === WGS library insert size values used for Illumina-only assembly ```csvpreview {header="false"} Mean,350 SD,77 ``` * Assembly output (only the primary) ```csvpreview {header="false"} N50,216580 Sequence,1220326965 Average,33478.6 E-size,277595 Count,36451 ``` :::warning Illumina-only assembly explain the fragmentation and low N50. Long reads are not enough for hybrid approach. ::: --- Pseudohaplotype.1 ![](https://i.imgur.com/aKr5hAy.png) Both pseudohaplotypes ![](https://i.imgur.com/DNzTprX.png) :::info The ammount of retained haplotypes looks low. ::: --- :::info :bulb: **Cutoffs:** ++Low++ coverage value marks that any contig with an average coverge less than that number is a junk contig, while ++high++ coverage value marks that contigs with an average coverage over that number are usually repeats. The ++middle++ value is the diploid coverage. > If there is a single peak, the first cutoff should be placed just leaving the valley, the middle cutoff at 0.75\*seq-coverage, and the last one at 3\*seq-coverage. We could try this using the sequencing coverage value from purge_dups (57). Other possibility is using the VGP recommendation of Transition parameter (33) for middle value and Maximum read depth (99) for high. ::: ![](https://i.imgur.com/TULTXZ4.png) `mean: 56, peak: 57, mean not larger than peak, treat as haploid assembly` * Assembly size comparison: |Assembly|purged (n)|haplotigs (n)| |---|:---:|:---:| |c1|1220.32 Mbp (36451)|-| |c2|16.71 Mbp (17562)|-| |cutoffs (default) 5-43-129|1210.30 Mbp (27022)|10.03 Mbp (9486)| |cutoffs 10-43-129 <--|1210.18 Mbp (26769)|10.14 Mbp (9740)| |cutoffs 10-43-171|1210.99 Mbp (27205)|9.38 Mbp (9304)| |cutoffs 12-43-171|1210.92 Mbp (27097)|9.40 Mbp (9414)| |cutoffs 10-43-99|1209.62 Mbp (26491)|10.71 Mbp (10019)| |cutoffs 5-33-99|1210.26 Mbp (26913)|10.06 Mbp (9594)| |cutoffs 10-33-99|1210.15 Mbp (26665)|10.18 Mbp (9843)| |cutoffs 12-33-99|1210.08 (26556)|10.24 Mbp (9954)| --- --- --- * BUSCO (aves_odb10) ||masurca.c1|cutoffs (default)|cutoffs* 10-43-129| |-|:-:|:-:|:-:| |Complete BUSCOs|7882|7879|7879| |Complete & single-copy BUSCOs|7841|7838|7838| |Complete & duplicated|41|41|41| |Fragmented|205|206|206| |Missing|251|253|253| |Total|8338|8338|8338| :::info Purge does not improve dramaticaly over c1. I'm going to use the softest (cutoffs 10-43-129) ::: c1c2 p1q2 merqury y toda la bola RagTag & LongStitch === p1 vs s1 |Assembly|p1|s1| |-|:-:|:-:| |# contigs (total)||| |# contigs (>= 5 Kbp)||| |# contigs (>= 25 Kbp)||| |Length (total)||| |Length (>= 5 Kbp)||| |Length (>= 25 Kbp)||| |Largest contig||| |Total length||| |Estimated reference length||| |GC (%)||| |N50||| |N75||| |L50||| |L75||| |# N's per 100 kbp||| ||p1|s1| |-|:-:|:-:| |Complete BUSCOs||| |Complete & single-copy BUSCOs||| |Complete & duplicated||| |Fragmented||| |Missing||| |Total||| |Assembly Name|QV|Completeness (%)| |-|:-:|:-:| |p1||| |s1||| 3D-DNA === s1 vs s2 |Assembly|s1|s2| |-|:-:|:-:| |# contigs (total)||| |# contigs (>= 5 Kbp)||| |# contigs (>= 25 Kbp)||| |Length (total)||| |Length (>= 5 Kbp)||| |Length (>= 25 Kbp)||| |Largest contig||| |Total length||| |Estimated reference length||| |GC (%)||| |N50||| |N75||| |L50||| |L75||| |# N's per 100 kbp||| ||s1|s2| |-|:-:|:-:| |Complete BUSCOs||| |Complete & single-copy BUSCOs||| |Complete & duplicated||| |Fragmented||| |Missing||| |Total||| |Assembly Name|QV|Completeness (%)| |-|:-:|:-:| |s1||| |s2||| DENTIST & PILON === |Assembly|s2|Pehuel.pri| |-|:-:|:-:| |# contigs (total)||| |# contigs (>= 5 Kbp)||| |# contigs (>= 25 Kbp)||| |Length (total)||| |Length (>= 5 Kbp)||| |Length (>= 25 Kbp)||| |Largest contig||| |Total length||| |Estimated reference length||| |GC (%)||| |N50||| |N75||| |L50||| |L75||| |# N's per 100 kbp||| ||s2|Pehue.pri| |-|:-:|:-:| |Complete BUSCOs||| |Complete & single-copy BUSCOs||| |Complete & duplicated||| |Fragmented||| |Missing||| |Total||| ### 093 | ASM_ID | Bases_Mb | GC_% | Scaff | Cont | Gaps | Longest_Scaff_Mb | Scaff_N50_Mb | Scaff L50 | Scaff_N95_Mb | Scaff L95 | Longest_Cont_Mb | Cont N50 | Cont L50 | Cont N95 | Cont L95 | QV | KComplet | BUSCO-C % | BUSCO-S % | hap | both Hap | shared | |:--------- | --------:| -----:| ---------:| ---------:| ------:| ----------------:| ------------:| ---------:| ------------:| ---------:| ---------------:| -----------:| --------:| -----------:| --------:| -----:| ------------:| -------------:| --------------------:| ------------------------------------ | -------- | ------ | | MaS | 1,219.46 | 42.36 | 38,187 | 43,005 | 4,818 | 1.51 | 0.19 | 0.19 | 0.02 | 0.02 | 0.99 | 0.14 | 0.14 | 0.02 | 0.02 | 50.14 | 97.72 | 94.2 | 93.7 | | | | | ALGA | 1,209.06 | 42.23 | 213,310 | 213,310 | 0 | 0.16 | 0.02 | 0.02 | 0 | 0 | 0.16 | 0.02 | 0.02 | 0 | 0 | inf | 97.55 | 61.9 | 61.7 | ![](https://i.imgur.com/62jYv2e.png) | - | - | | Plat | 1,369.29 | 43.46 | 2,098,110 | 2,098,110 | 0 | 0.14 | 0.01 | 0.01 | 0 | 0 | 0.14 | 0.01 | 0.01 | 0 | 0 | inf | 98.12 | 58.9 | 58.7 | | | | | Plat_Scaf | 1,254.98 | 42.62 | 649,266 | 730,697 | 81,431 | 0.83 | 0.06 | 0.06 | 0 | 0 | 0.23 | 0.02 | 0.02 | 0 | 0 | 66.36 | 98.03 | 88.2 | 87.9 | | | | | Plat_Gap | 1,255.45 | 42.62 | 649,266 | 686,184 | 36918 | 0.83 | 0.06 | 0.06 | 0 | 0 | 0.28 | 0.03 | 0.03 | 0 | 0 | 64.92 | 98.06 | 88.3 | 87.9 | | | | | ASM_ID | Total Mb | Scaf | Cont | Gaps | Gaps Mb | Longest Scaf | Scaf N50 | Scaf L50 | Scaf N95 | Scaf L95 | Longest Cont | Cont N50 | Cont L50 | Cont N95 | Cont L95 | QV | KCompl | BUSCO-C % | BUSCO-S % | |:---------- | --------:| ------:| ------:| ------:| --- | ----------------:| ------------:| -------------:| ------------:| -------------:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:| | AL.pur.Rag | 1,241.86 | 69,106 | 210,892 | 141,786 | 33.54 | 219.88 | 85.35 | 5 | 6.41 | 27 | 0.16 | 0.02 | 22,831 | 0 | 102,052 | 82.79 | 97.51 | 96.6 | 96.3 | | MA.pur.Rag | 1228.86 | 24605 | 41567 | 16962 | 11.46 | 70.32 | 16.53 | 24 | 0.95 | 109 | 1.08 | 0.16 | 2,301 | 0.02 | 10,339 | 50.14 | 97.63 | 97.1 | 96.8 | | PL.pur.Rag | 1279.74 | 545216 | 730531 | 185315 | 27.45 | 219.16 | 84.94 | 5 | 0 | 34,096 | 0.23 | 0.02 | 20,314 | 0 | 224,725 | 66.31 | 98.01 | 97.2 | 97 | | AL.Rag.pur | 1237.88 | 68307 | 205527 | 137220 | 32.78 | 219.89 | 85.4 | 5 | 6.4 | 27 | 0.16 | 0.02 | 22,724 | 0 | 100,562 | 82.78 | 97.42 | 96.6 | 96.3 | | MA.Rag.pur | 1226.77 | 24113 | 40279 | 16166 | 11.32 | 70.32 | 17.08 | 23 | 1.07 | 107 | 1.08 | 0.16 | 2,295 | 0.02 | 10,240 | 50.19 | 97.59 | 97.1 | 96.8 | | PL.Rag.pur | 1271.58 | 543737 | 706237 | 162500 | 24.41 | 219.15 | 84.81 | 5 | 0 | 35,255 | 0.23 | 0.02 | 20,170 | 0 | 203,494 | 66.32 | 97.86 | 97.2 | 97 | | ASM_ID | ASM_LEVEL | Bases_Mb | Est_Size_Mb | Het_% | GC_% | Scaff | Cont | Gaps | Longest_Scaff_Mb | Scaff_N50_Mb | Scaff_NG50_Mb | Scaff_N95_Mb | Scaff_NG95_Mb | Longest_Cont_Mb | Cont_N50_Mb | Cont_NG50_Mb | Cont_N95_Mb | Cont_NG95_Mb | QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% | |:---------|:------------|-----------:|--------------:|--------:|-------:|--------:|-------:|-------:|-------------------:|---------------:|----------------:|---------------:|----------------:|------------------:|--------------:|---------------:|--------------:|---------------:|------:|---------------:|----------------:|-----------------------:| | AL_yahs | scaff | 1222.45 | 1222.95 | 0.26 | 42.06 | 15324 | 152596 | 137272 | 219.89 | 85.4 | 85.4 | 7.65 | 7.65 | 0.16 | 0.02 | 0.02 | 0 | 0 | 82.73 | 97.21 | 96.6 | 96.3 | | MA_yahs | scaff | 1225.06 | 1222.95 | 0.26 | 42.31 | 18999 | 35391 | 16392 | 220.03 | 84.87 | 84.87 | 7.78 | 7.78 | 1.08 | 0.16 | 0.16 | 0.02 | 0.02 | 50.21 | 97.58 | 97.2 | 96.9 | | PL_yahs | scaff | 1201.75 | 1222.95 | 0.26 | 41.97 | 4105 | 166570 | 162465 | 219.15 | 85.4 | 84.81 | 8.48 | 7.69 | 0.23 | 0.02 | 0.02 | 0 | 0 | 66.11 | 97.05 | 97.2 | 97 |

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