ttubb

A tool for ENA metagenome submission (see https://github.com/ttubb/submg)

Built to run the nanopore read polisher nanopolish (https://github.com/jts/nanopolish)

Built to run https://github.com/rrwick/Deepbinner

Built to run https://github.com/nanoporetech/ont_fast5_api

Built to run the redbean assembler (formerly called wtdbg2) https://github.com/ruanjue/wtdbg2

Built to run the miniasm long read assembler (https://github.com/lh3/miniasm)

Built to run https://github.com/nanoporetech/qcat

Built to run https://github.com/ablab/quast

Built to run https://github.com/fenderglass/Flye/

Built to run https://github.com/wdecoster/nanoQC

Built to run the nanopore draft assembly polisher medaka (https://github.com/nanoporetech/medaka)

Built to run nanoplot (https://github.com/wdecoster/NanoPlot)

Built to run scripts by https://github.com/gringer for processing nanopore 1d2 sequencing data.

Built to run https://github.com/marbl/canu

Built to run https://github.com/samtools

built to run the minimap2 aligner (https://github.com/lh3/minimap2).

Built to run https://github.com/xiaochuanle/NECAT

built to run the graphmap long read mapper (https://github.com/isovic/graphmap)

Built to run https://github.com/isovic/racon

Built to run the MaSuRCA genome assembler (https://github.com/alekseyzimin/masurca).

built to run https://github.com/BenLangmead/bowtie2

Built to run https://github.com/broadinstitute/pilon

Built to run https://github.com/rrwick/Porechop

built to run https://github.com/rrwick/Unicycler