Mapping |
Hisat2 | https://github.com/DaehwanKimLab/hisat2 | Bioconda::hisat2 |
bwa mem2 | https://github.com/bwa-mem2/bwa-mem2 | Bioconda::bwa-mem2 |
minimap2 | https://github.com/lh3/minimap2 | Bioconda::minimap2 |
ngmlr | https://github.com/philres/ngmlr | Bioconda::ngmlr |
Pipeline |
pipeasm | https://github.com/itvgenomics/pipeasm | Not available |
Quality check |
FastQC | https://github.com/s-andrews/FastQC | Bioconda::fastqc |
PycoQC | https://github.com/a-slide/pycoQC | Bioconda::pycoqc |
MinionQC | https://github.com/roblanf/minion_qc | Bioconda::R-minionqc |
pychopper | https://github.com/epi2me-labs/pychopper | Bioconda::pychopper |
porechop_ABI | https://github.com/bonsai-team/Porechop_ABI | Bioconda::porechop_abi |
nanofilt | https://github.com/wdecoster/nanofilt | Bioconda::nanofilt |
HiFi Consensus |
DeepConsensus | https://github.com/google/deepconsensus | Not available |
Assembly |
Flye | https://github.com/mikolmogorov/Flye | Bioconda::flye |
wtdbg2 | https://github.com/ruanjue/wtdbg2 | Not available |
Canu/HiCanu | https://github.com/marbl/canu | Bioconda::canu |
Hifiasm | https://github.com/chhylp123/hifiasm | Bioconda::hifiasm |
Racon | https://github.com/isovic/racon | Bioconda::racon |
Miniasm | https://github.com/lh3/miniasm | Bioconda::miniasm |
Shasta | https://github.com/paoloshasta/shasta | Bioconda::shasta |
Necat | https://github.com/xiaochuanle/NECAT | Bioconda::necat |
smartdenovo | https://github.com/ruanjue/smartdenovo | Bioconda::smartdenovo |
Goldrush | https://github.com/bcgsc/goldrush | Bioconda::goldrush |
nextdenovo | https://github.com/Nextomics/NextDenovo | Bioconda::nextdenovo |
spades | https://github.com/ablab/spades | Bioconda::spades |
Contam. check |
FCS-GX | https://github.com/ncbi/fcs-gx | Bioconda::ncbi-fcs-gx |
blobtools | https://github.com/DRL/blobtools | Bioconda::blobtools |
blobtoolkit | https://github.com/blobtoolkit/blobtoolkit | Bioconda::blobtoolkit |
markerscan | https://github.com/CobiontID/MarkerScan | Not available |
Scaffolding |
SSPACE- LongRead | https://github.com/Runsheng/sspace_longread | Not available |
SSPACE | https://github.com/nsoranzo/sspace_basic | Bioconda::sspace_basic |
SLR | https://github.com/luojunwei/SLR | Etetoolkit::slr |
ARCS | https://github.com/bcgsc/arcs | Bioconda::arcs |
LRNA- scaffolder | https://github.com/CAFS-bioinformatics/L_RNA_scaffolder | Not available |
qc3 C | https://github.com/cerebis/qc3C | Bioconda::qc3c |
Picard | https://github.com/broadinstitute/picard | Bioconda::picard |
chromap | https://github.com/haowenz/chromap | Bioconda::chromap |
YaHS | https://github.com/c-zhou/yahs | Bioconda::yahs |
Telomeres |
tidk | https://github.com/tolkit/telomeric-identifier | Bioconda::tidk |
HiC visual |
Juicer | https://github.com/aidenlab/juicer | Bioconda::juicer |
Rapid curation | https://gitlab.com/wtsi-grit/rapid-curation | Not available |
Assembly quality |
quast/quast-LG | https://github.com/ablab/quast | Bioconda::quast |
Busco | https://gitlab.com/ezlab/busco | Bioconda::busco |
Compleasm | https://github.com/huangnengCSU/compleasm | Bioconda::compleasm |
Meryl | https://github.com/marbl/meryl | Bioconda::meryl |
Merqury | https://github.com/marbl/merqury | Bioconda::merqury |
Bamqc | https://github.com/s-andrews/BamQC | Bioconda::qualimap |
Haplopurging |
Redundans | https://github.com/Gabaldonlab/redundans | Bioconda::redundans |
purge_haplotigs | https://github.com/skingan/purge_haplotigs_multiBAM | Bioconda::purge_haplotigs |
purge_dups | https://github.com/dfguan/purge_dups | Bioconda::purge_dups |
HapSolo | https://github.com/esolares/HapSolo | Biocomda::hapsolo |
Repeats |
Repeatmasker | https://github.com/Dfam-consortium/RepeatMasker | Bioconda::repeatmasker |
Repeatmodeler | https://github.com/Dfam-consortium/RepeatModeler | Bioconda::repeatmodeler |
Annotation |
Augustus | https://github.com/Gaius-Augustus/Augustus | Bioconda::augustus |
Braker 3 | https://github.com/Gaius-Augustus/BRAKER | Bioconda::braker3 |
funannotate | https://github.com/nextgenusfs/funannotate | Bioconda::funannotate |
helixer | https://github.com/weberlab-hhu/Helixer | Not available |
Toga | https://github.com/hillerlab/TOGA | Not available |
interproscan | https://github.com/ebi-pf-team/interproscan | Bioconda::interproscan |
EggNOGmapper | https://github.com/eggnogdb/eggnog-mapper | Bioconda::eggnog-mapper |
Fantasia | https://github.com/MetazoaPhylogenomicsLab/FANTASIA | Not available |
