Commit c690b5e6 authored by Natasha Pavlovikj's avatar Natasha Pavlovikj
Browse files

Merge branch 'update_scythe' into 'master'

Update scythe documentation

See merge request !301
parents 56a1cb06 87204f7a
......@@ -14,7 +14,7 @@ $ scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq
{{< /highlight >}}
where **adapter_file.fasta** is fasta input file of the adapter sequences that need to be removed from the 3' end of the sequence data, and **input_reads.fastq** is the input sequencing data in fastq format.
The file **output_reads.fastq** contains the sequencing reads with removed adapters. If the adapter sequences are unknown, Scythe by itself provides two adapter sequences that can be used with the **-a** option: **illumina_adapters.fa** and **truseq_adapters.fasta**.
The file **output_reads.fastq** contains the sequencing reads with removed adapters. If the adapter sequences are unknown, Scythe by itself provides Illumina adapter sequences that can be used with the **-a** option: **illumina_adapters.fa**.
More information about Scythe can found by typing:
{{< highlight bash >}}
......@@ -36,13 +36,13 @@ Simple Scythe script that uses the `illumina_adapters.fa` file and `input_reads.
module load scythe/0.991
scythe -a ${SCYTHE_HOME}/illumina_adapters.fa input_reads.fastq -o output_reads.fastq
scythe -a ${SCYTHE_ADAPTERS}/illumina_adapters.fa input_reads.fastq -o output_reads.fastq
{{< /highlight >}}
{{% /panel %}}
Scythe is single threaded program, and therefore both `#SBATCH --nodes` and `#SBATCH --ntasks-per-node` are set to **1**.
The two adapter sequences provided by Scythe are stored in **$SCYTHE_HOME**. Hence, to access the illumina adapter file use: `$SCYTHE_HOME/illumina_adapters.fa`, and to access the TruSeq file use: `$SCYTHE_HOME/truseq_adapters.fasta`.
The Illumina adapter sequences provided by Scythe are stored in **$SCYTHE_ADAPTERS**. Hence, to access the illumina adapter file use: `$SCYTHE_ADAPTERS/illumina_adapters.fa`.
### Scythe Output
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