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Commit d385875f authored by peguerin's avatar peguerin
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table results

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README.md
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......@@ -22,7 +22,7 @@ A collection of commands to assemble genome from NGS data.
We aims to assemble 3 _de novo_ draft genomes of one invididual of 3 different species
- _Diplodus sargus_ that we refers as `sar`
- _Mullus surmuletus as `mullus`
- _Mullus surmuletus_ as `mullus`
- _Serranus cabrilla_ as `serran`
......@@ -51,8 +51,6 @@ The three draft genomes were sequenced within the NGS technology.
## Set the initial directory structure
main folder
- pe-dir
- 180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
- 180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
......@@ -68,6 +66,7 @@ main folder
- Lib_10_S1_L002_R1_001.fastq
- Lib_10_S1_L002_R2_001.fastq
with `pe-dir` as a folder of paired-end sequencing results, `me-dir` as mate-pair and `x-dir` as linked-reads.
......@@ -75,6 +74,8 @@ main folder
## Platanus
### assemble contig
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......@@ -97,3 +98,23 @@ fff
# Results
Species | Genome assembler | Computing platform | Library | # of contigs | Contig N50 | Total size
(Mbp) | # of scaffolds | Scaffold N50 | Coverage
--------------------|--------------------|----------------------|---------------------------------------------------------------------------|----------------|--------------|--------------------|------------------|----------------|----------
Diplodus sargus
| Platanus | MBB | Paired-end 350bp & 550bp insert size
Mate-pair 3Kbp & 5Kbp insert size
| 3030501 | 991 | 856 | 4227 | 2660334 | 53X
| Platanus | MESO@LR | | 2408078 | 1101 | 785 | 2344 | 3371708 | 57X
Mullus surmuletus
| Platanus | MBB | | 3616310 | 344 | 653 | 5417 | 192808 | 69X
| Platanus | MESO@LR | | 3146055 | 384 | 613 | 2940 | 488370 | 74X
| Abyss2 | MBB | | 36011115 | 96 | 686 | 4938 | 17739 | 66X
Serranus cabrilla
| Platanus | MBB | | 2169385 | 1135 | 627 | 2190 | 613541 | 63X
| Supernova | MESO@LR | Chromium
linked-reads | NA | NA | 223 *
| 4951 * | 67074 * |
| ARCS | MBB | Both | NA | NA | 627 | 2122 | 624679 | 63X
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