Nipah virus vector sequences in COVID-19 patient samples sequenced by the Wuhan Institute of Virology

Supplementary material including:

Supp. Figs.

Supp_Figs.pdf

Supp. Data

1_Datasets_and_Alignments.xlsx: Dataset details, fastv analysis results, alignment statistics, read counts and coverage.

2_AY988601_1_MGISEQ_L04_reads_MSA_view.png: Pooled reads from SRR11092059, SRR11092060, SRR11092061, SRR11092062 (Lane 4), SRR11092063 (Lane 4) aligned with bwa mem. Consensus generated in IGV then aligned using BLASTN to AY988601.1 and plotted in MSA viewer.

3_AY988601_1_MGISEQ_L04_reads_synthetic_ends_blast.fa: Identifiable synthetic ends to reads from pooled reads from SRR11092059, SRR11092060, SRR11092061, SRR11092062 (Lane 4), SRR11092063 (Lane 4) aligned with bwa mem. 

4_AY988601_1_BLASTN_default_hits.fa: BLASTN of AY988601.1 against the following search set: SRR11092059, SRR11092060, SRR11092061, SRR11092062, SRR11092063 using max target sequences of 1000.

5_AY988601_1_MGISEQ_L04_MEGAHIT_contigs_all.sam: MEGAHIT de novo assembled contigs from SRR11092059, SRR11092060, SRR11092061, SRR11092062 (Lane 4), SRR11092063 (Lane 4), aligned with bwa mem to AY988601.1.

6_AY988601_1_SRR11092059_MEGAHIT_k79_contigs.sam: MEGAHIT de novo assembled k79 mer contigs from SRR11092059 aligned with bwa mem to AY988601.1.

7_AY988601_1_MGISEQ_L04_coronaSPAdes_contigs_all.sam: CornaSPAdes de novo assembled contigs from SRR11092059, SRR11092060, SRR11092061, SRR11092062 (Lane 4), SRR11092063 (Lane 4), aligned with bwa mem to AY988601.1.