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Jean Elbers jelber2

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jelber2 / Plot_Animated_Nanopore_Quality_x_Length_2D_Contours.jl
Created May 10, 2024 12:07
Makes an animated plot of read quality and read length density contours over time for Nanopore Dorado basecalled, indexed BAM files
using XAM
using ArgParse
using DataFrames
using Dates
using Statistics
using Base.MathConstants
using StatsBase
using StatsPlots
using KernelDensity
@jelber2
jelber2 / PlotQualityHistogram.jl
Last active May 8, 2024 12:42
Plots Quality Score Density Distribution per Hour of a Sequencing Run
# note: the Dorado BAM file produced by basecalling POD5 files needs to be indexed with "samtools index input_file"
# note2: something seems really strange about the qualtiy scores, I have checked several times, but they seem correct
# I am not sure why they are reporting that for example reads with Q38 average quality scores.
# EDIT: this is fixed, see https://www.biostars.org/p/295932/#295936 for better formula for average Phred Score
# tested with julia-1.10.3 and XAM.jl-0.40
using XAM
using ArgParse
using DataFrames
using Dates
using Plots
@jelber2
jelber2 / changeBAMquality.jl
Created April 30, 2024 08:56
Converts quality scores in BAM alignments to a single ASCII Phred Score you desire
# note: outputs to STDOUT a SAM file without a header
# note2: remove auxillary tags and information
# note3: ignores RNEXT and PNEXT from BAM file (puts * and 0 respectivelv)
# tested with julialang v1.10.2 and XAM v0.4.0
# $ julia changeBAMquality.jl input.bam ? > test.sam.noheader
#
# to add a header from the original BAM file that had its qualities changed
# and add on a PG line
# $ ASCII_CHARACTER="?"
# $ INPUT=input.bam
@jelber2
jelber2 / PlotSequenceTime.jl
Last active March 26, 2024 10:04
Plot changes in read length distribution of Nanopore Dorado called bases
using XAM
using ArgParse
using DataFrames
using Dates
using Plots
using StatsBase
using Plots.PlotMeasures
function parse_commandline()
@jelber2
jelber2 / stitch-fasta.jl
Last active March 7, 2024 09:45
Stitch FASTA reads shredded with shred.sh from BBTools back together
# tested on Julialang v.1.10.2, DataStructures v0.18.16, and FASTX v2.1.4
# Usage
# $ julia stitch-fasta.jl chr20.herro.fasta.Q30.recal.shred.fasta > chr20.herro.fasta.Q30.recal.fasta
#
import Pkg; Pkg.add("FASTX")
import Pkg; Pkg.add("DataStructures")
using DataStructures
using FASTX
function process_fasta_file(filename::String)
@jelber2
jelber2 / stitch-fastq.jl
Last active March 7, 2024 09:45
Stitch FASTQ reads shredded with shred.sh from BBTools back together
# tested on Julialang v.1.10.2 , DataStructures v0.18.16, and FASTX v2.1.4
# Usage
# $ julia stitch-fastq.jl chr20.herro.fasta.Q30.recal.shred.fastq > chr20.herro.fasta.Q30.recal.fastq
#
import Pkg; Pkg.add("FASTX")
import Pkg; Pkg.add("DataStructures")
using DataStructures
using FASTX
function process_fastq_file(filename::String)
@jelber2
jelber2 / shredBAM.jl
Last active March 11, 2024 13:09
Shred alignments in a BAM file (output is a SAM file without header) to make long read alignments into short-read-like
# previous versions allowed to generate directly from BAM, but there seemed to have been some troubles
# between versions of XAM, so this version is working so far for its intended purpose on https://github.com/brendanofallon/jovian
# also, this version is rather fast
#
#
# note: ignores quality scores at the moment - fixed in revision#4
# note2: outputs to STDOUT a SAM file without a header
# tested with julialang v1.10.2 and XAM v0.4.0
# $ julia shredBAM.jl input.bam 300 > test.sam.noheader
#
@jelber2
jelber2 / README.txt
Last active February 29, 2024 10:25
Error_rates_in_Herro_and_corrected_Herro_reads_compared_to_NextSeq2000
# output from best commit #fcdfa97 (https://github.com/google/best), .summary_identity_stats.csv files using reads
# aligned to concatenated chr20_MATERNAL and chr20_PATERNAL from hg002v1.0.1.fasta.gz (https://github.com/marbl/HG002) (https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.0.1.fasta.gz)
# using mm2-fast commit # 10bde16 using settings: --eqx --secondary=no -Y -c -ax map-ont -k 19 -w 13 -t 48
# or using these settings for Illumina NextSeq2000 reads: -t 48 --eqx --secondary=no -acx sr
#
# brutal_rewrite (br) commit # ad87f92 (https://github.com/natir/br) using settings: -k 19 -m graph
# kmer read filter (kmrf) commit # 36cad24 (https://github.com/natir/kmrf) using setting: -k 17
# peregrine-2021 (pg_asm) commit # 6698eb1 (https://github.com/cschin/peregrine-2021): using default settings
#
# herro (herro) commit # c41dc30 (https://github.com/lbcb-sci/herro) using defaults and model at time of commit
@jelber2
jelber2 / README.md
Last active October 18, 2023 13:41
MethPhaser

MethPhaser installation

Install micromamba or mamba or conda

# Install micromamba
"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

You will then see something like this in a BASH shell (parts with "(type....)" are added for instructions

@jelber2
jelber2 / gist:451eec8c6b74617b8bf0532905f256c1
Last active October 25, 2023 09:51
Zymo_Mock_HMW_SUP_duplex_reads_with_peregrine_2021
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