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 …

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

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

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.

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.

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

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

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.

A tool to index and extract data from gzipped FASTQ files

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

Sanyojan is a highly sensitive, hybrid genome assembler.