Skip to content

Commit cc5f6f1

Browse files
committed
more typo fix
1 parent 44f28ea commit cc5f6f1

File tree

1 file changed

+2
-2
lines changed

1 file changed

+2
-2
lines changed

docs/output.md

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -184,7 +184,7 @@ BAM files containing the original alignments from either Minimap2 or BWA are fur
184184

185185
</details>
186186

187-
[BCFtools](http://samtools.github.io/bcftools/bcftools.html) is a set of utilities that manipulate variant calls in [VCF](https://vcftools.github.io/specs.html) and its binary counterpart BCF format. It can also used be used to generate statistics and counts obtained from VCF files as used here.
187+
[BCFtools](http://samtools.github.io/bcftools/bcftools.html) is a set of utilities that manipulate variant calls in [VCF](https://vcftools.github.io/specs.html) and its binary counterpart BCF format. It can also be used to generate statistics and counts obtained from VCF files as used here.
188188

189189
![MultiQC - BCFTools variant counts](images/mqc_bcftools_stats_plot.png)
190190

@@ -703,7 +703,7 @@ As described in the [iVar variants](#ivar-variants) section, iVar can be used in
703703

704704
</details>
705705

706-
[BCFTools](http://samtools.github.io/bcftools/bcftools.html) is used in the variant calling and _de novo_ assembly steps of this pipeline to obtain basic statistics from the VCF output. It can also used be used to generate a consensus sequence by integrating variant calls into the reference genome. In this pipeline, we use `samtools mpileup` to create a mask using low coverage positions, and `bedtools maskfasta` to mask the genome sequences based on these intervals. Finally, `bcftools consensus` is used to generate the consensus by projecting the high allele frequency variants onto the masked genome reference sequence.
706+
[BCFTools](http://samtools.github.io/bcftools/bcftools.html) is used in the variant calling and _de novo_ assembly steps of this pipeline to obtain basic statistics from the VCF output. It can also be used to generate a consensus sequence by integrating variant calls into the reference genome. In this pipeline, we use `samtools mpileup` to create a mask using low coverage positions, and `bedtools maskfasta` to mask the genome sequences based on these intervals. Finally, `bcftools consensus` is used to generate the consensus by projecting the high allele frequency variants onto the masked genome reference sequence.
707707

708708
### QUAST
709709

0 commit comments

Comments
 (0)