Scalable long read self-correction and assembly polishing with multiple sequence alignment

Collection of blogs/publications by Nepali devs.

Standalone tool and library allowing to work with barcoded linked-reads

A Raspberry Pi Simple python Stand Alone Local Network Web Server. Automatically reads folder and file entries into a right pane selection list. Selected folder opens a new browser tab and Selected file displays content in browser left pane iframe. Right pane list can be ordered by date/time or alphabetic ascending or descending via settings.py …

Assembled Phi-X174 genome using Overlap Graph, Kmer Composition and De-Bruijn Graph.

Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads

Study material (pdfs, notes, free course download links etc) for HACKERS

Ancient DNA Read Simulator for Metagenomic

Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, …

Genome read alignments visualizer

📚 A list of physical books I own or want to read.

Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5

The Clip&Merge Method for paired end read merging and adapter clipping, quality trimming and other FastQ operations.

Preprocessing of raw reads obtained using ARTIC's protocol for sequencing SARS-CoV-2 genome.

Software for cleaning fastq reads with or without adapter list

Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.

Filter alignments on sequence length and/or identity of first nucleotide.

Sanyojan is a highly sensitive, hybrid genome assembler.

Temperature, Relative Humidity, Atmospheric Pressure Logger program, displays and saves data to a csv file

R functions and workflow for submitting amplicon sequence data to the ENA.