Chris:LabNotes/Microbiome/2011/2011-5-2
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Slide Shortening Assembly Test
Background
- Sam tried to increase SAG contig length by using recruited sequences from metagenomic contigs (http://genome-tech.ucsd.edu/LabNotes/index.php/Sam:LabNotes/Microbiome-new/2011-4-19)
- But results showed some decreased contig lengths after recruitment (ID2, ID9, ID11)
- Dr. Zhang suggested that the decreased contig lengths may be fixed by slide shortening of contigs
- On 4/29, I wrote perl script that could help perform the slide shortening of contigs
- Here, I test the script/method of slide shortening to increase the contig length after recruitment
- SAG sequence: ID9 because showed the lower contig length but showed relatively good contig length
- Sequences found in: </media/disk-1/samchiang/Sub_tests_folder_imp/2_Extending_Mouse_Bac_SAG_contigs/BLAT_Meta2SAG_040311/Step4_pooled_together/SAG_A_ID9>
- Test found in: </media/disk-2/cjwei/slide-shortening_Assembly_Test>
- Used various sliding cut lengths:
- Test 1: >1000bp contigs cut; step size = 200bp
- Test 2: >2000bp contigs cut; step size = 100bp (same as "Whole Genome Amplification and Denovo Assembly of Single Bacterial Cells")
- Test 3: >1000bp contigs cut; step size = 100bp
- Test 4: >100bp contigs cut; step size = 10bp (most highly cut option)
- Also tried out the sliding cut on best assembly (see if can improve the best recruited assembly results) = ID3
- Tested >2000bp contigs cut; step size = 100bp (was shown with ID9 that this produced highest N50 and highest sum)
Procedure
- Use Sliding Cut for combined SAG and recruited metagenome contigs:
perl contig_sliding_cut.pl SAG_A_ID9_and_recruted_Meta_all >SAG_A_ID9_and_recruted_Meta_all_slide_cut
- Run Velveth
- k-mer 27, -short
/media/disk-2/cjwei/Velvet/velveth SAG_A_ID9_and_recruted_Meta_all_slide_cut_Assembly/ 27 -fasta -short SAG_A_ID9_and_recruted_Meta_all_slide_cut
- Run Velvetg
- fixed setting as cov_cutoff 2, min-contig lgth 100
/media/disk-2/cjwei/Velvet/velvetg SAG_A_ID9_and_recruted_Meta_all_slide_cut_Assembly/ -cov_cutoff 2 -min_contig_lgth 100
Results
ID9 (problem assembly)
n n:100 n:N50 min median mean N50 max sum 7871 7871 737 100 196 465 1000 20981 3662057 contigs_1000_200.fa 7819 7819 710 100 197 473 1057 21081 3703868 contigs_2000_100.fa 7861 7861 726 100 196 469 1039 21081 3689257 contigs_1000_100.fa 7869 7869 718 100 196 468 1041 21091 3690448 contigs_100_10.fa 14828 14828 1140 100 170 403 902 38317 5988190 ../SAG_A_ID9_and_recruted_Meta_all
- Based on results, notice that >2000bp contigs cut; step size = 100bp had highest N50 and sum (with relatively the same number of contigs formed -> slightly fewer may be because less short contigs?)
ID3 (best assembly)
n n:100 n:N50 min median mean N50 max sum 1818 1818 123 100 276 1270 4712 54000 2309329 contigs.fa 6232 6232 471 100 276 2816 10646 54047 17.55e6 ../SAG_A_ID3_and_recruted_Meta_all