jelber2

# Get HG002
# wget https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.0.1.fasta.gz
# gunzip hg002v1.0.1.fasta.gz
#
# Use seqtk to get maternal and paternal sequences
# https://github.com/lh3/seqtk
# seqtk seq -l0 hg002v1.0.1.fasta|paste - - |fgrep "MATERNAL" |tr '\t' '\n'|seqtk seq -l60 > hg002v1.0.1.maternal.fasta &
# seqtk seq -l0 hg002v1.0.1.fasta|paste - - |fgrep "PATERNAL" |tr '\t' '\n'|seqtk seq -l60 > hg002v1.0.1.paternal.fasta &
#
# use samtools to index haplotypes

jelber2

# new in revision 2, multithreaded support - up to twice as fast as single-threaded, revision 1
# invoke with:

# julia --threads 16 Plot_Animated_Nanopore_Quality_x_Length_2D_Contours.jl --input_file test.bam --fps 0.7 --output_file test.gif

# but need a lot of threads (up to 16, above 16 threads, get saturation in cores vs. time plot) 

using XAM
using ArgParse
using DataFrames

jelber2

# 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

# 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

using XAM
using ArgParse
using DataFrames
using Dates
using Plots
using StatsBase
using Plots.PlotMeasures


function parse_commandline()

jelber2

# 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

# 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

# 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

# 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

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