Anchr - the Assembler of N-free CHRomosomes
Current release: 0.3.18
# Via cargo
cargo install --path . --force #--offline
cargo install --git https://github.com/wang-q/anchr --branch main
# test
cargo test -- --test-threads=1
## Static binary for Linux
#mkdir -p ${HOME}/bin
#curl -fsSL $(
# curl -fsSL https://api.github.com/repos/wang-q/anchr/releases/latest |
# jq -r '.assets[] | select(.name == "anchr-x86_64-unknown-linux-musl.tar.gz").browser_download_url'
# ) |
# tar xvz
#cp target/x86_64-unknown-linux-musl/release/anchr ${HOME}/bin
#rm -fr target
# build under WSL 2
mkdir -p /tmp/cargo
export CARGO_TARGET_DIR=/tmp/cargo
cargo build
# build for CentOS 7
# rustup target add x86_64-unknown-linux-gnu
# pip3 install cargo-zigbuild
cargo zigbuild --target x86_64-unknown-linux-gnu.2.17 --release
ll $CARGO_TARGET_DIR/x86_64-unknown-linux-gnu/release/
$ anchr help
Anchr - the Assembler of N-free CHRomosomes
Usage: anchr [COMMAND]
Commands:
anchors Select anchors (proper covered regions) from contigs
contained Discard contained unitigs
covered Covered regions from .ovlp.tsv files
dazzname Rename FASTA records for dazz_db
dep Dependencies
ena ENA scripts
merge Merge overlapped unitigs
mergeread Merge Illumina PE reads with bbtools
orient Orient overlapped sequences to the same strand
overlap Detect overlaps by daligner
paf2ovlp Convert minimap .paf to overlaps
quorum Run quorum to discard bad reads
restrict Restrict overlaps to known pairs
show2ovlp Convert LAshow outputs to overlaps
template Creates Bash scripts
trim Trim Illumina PE/SE fastq files
unitigs Create unitigs from trimmed/merged reads
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
- Command line tools managed by
Homebrew
brew install perl cpanminus
brew install r
brew install parallel pigz
# cite parallel
# echo "will cite" | parallel --citation
cargo install intspan
cargo install fd-find
curl -LO https://github.com/brentp/mosdepth/releases/download/v0.3.10/mosdepth
chmod +x mosdepth
mv mosdepth ~/bin/
brew tap wang-q/tap
brew install wang-q/tap/tsv-utils
brew install --HEAD wang-q/tap/dazz_db
brew install --HEAD wang-q/tap/daligner
anchr dep install | bash
anchr dep check | bash
# Optional: fastk and fastga
brew install --HEAD wang-q/tap/fastk
brew install --HEAD wang-q/tap/merquryfk
brew install --HEAD wang-q/tap/fastga
brew install binutils
brew link binutils --force
parallel -j 1 -k --line-buffer '
Rscript -e '\'' if (!requireNamespace("{}", quietly = FALSE)) { install.packages("{}", repos="https://mirrors.tuna.tsinghua.edu.cn/CRAN") } '\''
' ::: \
argparse minpack.lm \
ggplot2 scales viridis
# Optional
# quast - assembly quality assessment
curl -LO https://github.com/ablab/quast/releases/download/quast_5.3.0/quast-5.3.0.tar.gz
tar xvfz quast-5.3.0.tar.gz
cd quast-5.3.0
python3 ./setup.py install
quast.py --test
# Optional: leading assemblers
brew install brewsci/bio/megahit
brew install spades
spades.py --test
brew install brewsci/bio/busco
mkdir -p ~/data/anchr/test
cd ~/data/anchr/test
# Lambda
for F in R1.fq.gz R2.fq.gz; do
1>&2 echo ${F}
curl -fsSLO "https://raw.githubusercontent.com/wang-q/anchr/main/tests/Lambda/${F}"
done
# trim
mkdir -p trim
pushd trim
anchr trim \
../R1.fq.gz ../R2.fq.gz \
-q 25 -l 60 \
-o stdout |
bash
popd
# merge read
mkdir -p merge
pushd merge
anchr mergeread \
../trim/R1.fq.gz ../trim/R2.fq.gz ../trim/Rs.fq.gz \
--ecphase "1 2 3" \
--parallel 4 \
-o stdout |
bash
popd
# quorum
pushd trim
anchr quorum \
R1.fq.gz R2.fq.gz \
-o stdout |
bash
popd
pushd trim/Q25L60
anchr quorum \
R1.fq.gz R2.fq.gz Rs.fq.gz \
-o stdout |
bash
popd
# unitigs - bcalm
mkdir -p bcalm
pushd bcalm
anchr unitigs \
../trim/pe.cor.fa ../trim/env.json \
-u bcalm \
--kmer "31 41 51 61 71 81" \
--parallel 4 \
-o unitigs.sh
bash unitigs.sh
popd
# anchors
mkdir -p bcalm/anchors
pushd bcalm/anchors
anchr anchors \
../unitigs.fasta \
../pe.cor.fa \
--readl 150 \
--keepedge \
-p 4 \
-o anchors.sh
bash anchors.sh
popd
# unitigs - superreads
gzip -dcf trim/pe.cor.fa.gz > trim/pe.cor.fa
mkdir -p superreads
pushd superreads
anchr unitigs \
../trim/pe.cor.fa ../trim/env.json \
--kmer "31 41 51 61 71 81" \
--parallel 4 \
-o unitigs.sh
bash unitigs.sh
popd
# unitigs - tadpole
mkdir -p tadpole
pushd tadpole
anchr unitigs \
../trim/pe.cor.fa ../trim/env.json \
-u tadpole \
--kmer "31 41 51 61 71 81" \
--parallel 4 \
-o unitigs.sh
bash unitigs.sh
popd
- Data source: Mycoplasma genitalium G37
mkdir -p ~/data/anchr/g37/ena
cd ~/data/anchr/g37/ena
cat << EOF > source.csv
ERX452667,G37,MiSeq
EOF
anchr ena info | perl - -v source.csv > ena_info.yml
anchr ena prep | perl - ena_info.yml
rgr md ena_info.tsv --fmt
aria2c -j 4 -x 4 -s 2 -c --file-allocation=none -i ena_info.ftp.txt
md5sum --check ena_info.md5.txt
## sampling reads as test materials
#seqtk sample -s 23 SRR5042715_1.fastq.gz 20000 | pigz > R1.fq.gz
#seqtk sample -s 23 SRR5042715_2.fastq.gz 20000 | pigz > R2.fq.gz
| name | srx | platform | layout | ilength | srr | spots | bases |
|---|---|---|---|---|---|---|---|
| G37 | ERX452667 | ILLUMINA | PAIRED | 447 | ERR486835 | 680,644 | 97.37M |
With a conventional directory structure, anchr template creates all scripts from reads QC to
assembly evaluations.
-
Model bacteria
-
FDA-ARGOS bacteria
-
Yeast
anchr dazzname tests/ovlpr/1_4.anchor.fasta -o stdout
anchr show2ovlp tests/ovlpr/1_4.show.txt tests/ovlpr/1_4.replace.tsv --orig
anchr paf2ovlp tests/ovlpr/1_4.pac.paf
echo "tests/ovlpr/1_4.anchor.fasta;tests/ovlpr/1_4.pac.fasta" |
parallel --colsep ";" -j 1 "
minimap2 -cx asm20 {1} {2} |
anchr paf2ovlp stdin |
tsv-sort
minimap2 -cx asm20 {2} {1} |
anchr paf2ovlp stdin |
tsv-sort
" |
anchr covered stdin --mean
anchr covered tests/ovlpr/1_4.pac.paf.ovlp.tsv
anchr covered tests/ovlpr/11_2.long.paf --paf
anchr covered tests/ovlpr/1_4.pac.paf.ovlp.tsv --base
anchr covered tests/ovlpr/1_4.pac.paf.ovlp.tsv --mean
anchr restrict tests/ovlpr/1_4.ovlp.tsv tests/ovlpr/1_4.restrict.tsv
anchr overlap tests/ovlpr/1_4.pac.fasta
anchr overlap tests/ovlpr/1_4.pac.fasta --idt 0.8 --len 2500 --serial
anchr orient tests/ovlpr/1_4.anchor.fasta tests/ovlpr/1_4.pac.fasta
anchr orient tests/ovlpr/1_4.anchor.fasta tests/ovlpr/1_4.pac.fasta -r tests/ovlpr/1_4.2.restrict.tsv
anchr contained tests/ovlpr/contained.fasta
cargo run --bin anchr merge tests/ovlpr/merge.fasta -o test.fasta
cargo run --bin anchr overlap2 tests/ovlpr/1_4.anchor.fasta tests/ovlpr/1_4.pac.fasta -d tmp
Qiang Wang [email protected]
Copyright by Qiang Wang.
MIT
Written by Qiang Wang [email protected], 2020-.