COVID-19: read pre-processing
Version 1

Galaxy version of pre-processing of reads from COVID-19 samples.

QC + human read cleaning

Based on https://github.com/Finn-Lab/Metagen-FastQC/blob/master/metagen-fastqc.sh

Inputs

ID Name Description Type
Forwards reads Forwards reads n/a n/a
Reverse reads Reverse reads n/a n/a
singlePaired singlePaired runtime parameter for tool Trim Galore! n/a
singlePaired singlePaired runtime parameter for tool Trim Galore! n/a
fastq_input fastq_input runtime parameter for tool Map with BWA-MEM n/a
fastq_input fastq_input runtime parameter for tool Map with BWA-MEM n/a
bed_file bed_file runtime parameter for tool Filter SAM or BAM, output SAM or BAM n/a

Steps

ID Name Description
0 Forwards reads
1 Reverse reads
2 Trim Galore! toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1
3 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
4 Filter SAM or BAM, output SAM or BAM toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1
5 Filtered reads toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1

Outputs

ID Name Description Type
trimmed_reads_pair1 trimmed_reads_pair1 n/a input
trimmed_reads_pair2 trimmed_reads_pair2 n/a input
bam_output bam_output n/a bam
output1 output1 n/a sam
forward forward n/a fasta
reverse reverse n/a fasta
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Views: 84   Downloads: 4

Created: 2nd Feb 2021 at 19:06

Last used: 15th Apr 2021 at 22:50

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Version 1 Created 2nd Feb 2021 at 19:06 by ignacio eguinoa

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