Wei Shen shenwei356

Functions:

# encoding: ACTG

def nuc2int_nochecking(b):
    return (ord(b) >> 1) & 3, True
    
def nuc2int_if(b):
    if b == 'a' or b == 'c' or b == 'g' or b == 't' \

or b == 'A' or b == 'C' or b == 'G' or b == 'T':

  8            .          .           TEXT ·__mm_add_epi32(SB),0,$0 
  9        640ms      640ms               VMOVDQU x+0(FP), Y0 
 10        5.62s      5.62s               VMOVDQU y+32(FP), Y1 
 11        4.81s      4.81s               VPADDD  Y1, Y0, Y0 
 12        1.16s      1.16s               VMOVDQU Y0, q+64(FP) 
 13        1.30s      1.30s               VZEROUPPER

14 . . RET

pandoc -f markdown -t html -c pandoc.css -s -o report.html

moved to Effect of random seed on results of seqkit sample

URL list

$ head choose_ftp.txt
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/405/GCA_000015405.1_ASM1540v1
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/620/625/GCA_000620625.1_ASM62062v1
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/972/925/GCA_000972925.1_ASM97292v1
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/021/385/GCA_001021385.1_ASM102138v1
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/328/565/GCA_000328565.1_ASM32856v1

Target files

Filtering Spades assembly result according to coverage information in sequence header

Sample sequence

$ cat contigs.fasta 
>NODE_1_length_869844_cov_1135.34
ACTGNacgtn 
>NODE_2_length_576386_cov_975.882
acgtn

	package main

	import (
	"compress/gzip"
	"fmt"
	"os"
	"strconv"

	boom "github.com/tylertreat/BoomFilters"
	)

	#!/bin/sh

	while read file; do
	if [[ $string =~ .=. ]]; then
	continue
	fi

	t=$(exiftool "$file" \
	\| grep "^Create Date" \| head -n 1 \
	\| sed -r "s/\s+/ /g" \| cut -d " " -f 4 \

	#!/bin/sh

	# Test data
	#
	# Retrieve 1M reads from any Illumina reads
	#
	# seqkit head -n 1000000 xxxx_1.fq.gz -o test.fq.gz
	#
	# Or
	#

	# Hello, and welcome to makefile basics.
	#
	# You will learn why `make` is so great, and why, despite its "weird" syntax,
	# it is actually a highly expressive, efficient, and powerful way to build
	# programs.
	#
	# Once you're done here, go to
	# http://www.gnu.org/software/make/manual/make.html
	# to learn SOOOO much more.