module load bbtools/38.82
module load bcftools/1.14
bbduk.sh threads=8 \
in1=raw/170283.mate1.fastq.gz \
in2=raw/170283.mate2.fastq.gz \
out1=fastq/170283-trimmed.mate1.fastq.gz \
out2=fastq/170283-trimmed.mate2.fastq.gz \
Jean Elbers jelber2
jelber2
/ gist:451eec8c6b74617b8bf0532905f256c1
Last active
October 25, 2023 09:51
Zymo_Mock_HMW_SUP_duplex_reads_with_peregrine_2021
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| This was with https://zymo-files.s3.amazonaws.com/BioPool/ZymoBIOMICS.STD.refseq.v2.zip | |
| RAW_SUP_Duplex pg_asm_1x_corrected_SUP_duplex pg_asm_2x_corrected_SUP_duplex pg_asm_3x_corrected_SUP_duplex | |
| Bacillus_subtilis Bacillus_subtilis Bacillus_subtilis Bacillus_subtilis | |
| # target bases: 4041255 # target bases: 4041255 # target bases: 4041255 # target bases: 4041255 | |
| # target bases overlapping regions: 4041255 (100.00%) # target bases overlapping regions: 4041255 (100.00%) # target bases overlapping regions: 4041255 (100.00%) # target bases overlapping regions: 4041255 (100.00%) | |
| 1159311 reference bases covered by exactly one contig 3791080 reference bases covered by exactly one contig 3642732 reference bases covered by exa |
jelber2
/ worm-adapter-trimming.md
Created
August 10, 2022 10:34
jelber2
/ pilon-runs-1-2.sh
Last active
November 9, 2018 08:31
Runs Pilon twice on a file called genome.pilon-0.fasta
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| #! /bin/bash | |
| set -e | |
| # installing fasta-splitter.pl | |
| ## wget http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.6.zip | |
| ## unzip fasta-splitter-0.2.6.zip | |
| # assumes initial genome to be error-corrected by pilon is called | |
| ## genome.pilon-0.fasta |
jelber2
/ Running-PBJelly-example-with-indel-correction-with-BBMap-no-Pilon.txt
Last active
November 9, 2018 08:34
Running-PBJelly-example-with-indel-correction-with-BBMap-no-Pilon
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| # goes along with http://seqanswers.com/forums/showthread.php?p=220925#post220925 | |
| # | |
| # assumes you have PBJelly, blasr, tabix, bcftools, samtools installed | |
| # below I am using a machine with 70 cores on a single node, adjust to the number of cores to your machine | |
| # The scripts below are obviously not designed for use with a cluster, but can be modified | |
| # | |
| ######################### | |
| # STEP 1 Combine the FASTQ files and remove the originals to save space | |
| ######################### | |
| ## first combine files and delete the originals to save space |
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